Mercurial > repos > bgruening > trim_galore
annotate trim_galore.xml @ 16:cd7e644cae1d draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
author | bgruening |
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date | Fri, 08 Oct 2021 09:57:52 +0000 |
parents | 084bbd8ba7b8 |
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rev | line source |
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16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
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1 <tool id="trim_galore" name="Trim Galore!" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
9
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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2 <description>Quality and adapter trimmer of reads</description> |
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11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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3 <macros> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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4 <import>macros.xml</import> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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5 </macros> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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6 <expand macro="requirements" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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7 <expand macro="xrefs"/> |
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f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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8 <version_command> |
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80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents:
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9 trim_galore --version |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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10 </version_command> |
13
b6c00b82f623
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit be11349529528f508eb05073396e80c3d1cbed4d
bgruening
parents:
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11 <command detect_errors="aggressive"><![CDATA[ |
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b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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12 #set compressed = 'no' |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
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13 #if $singlePaired.sPaired == "single": |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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14 #if $singlePaired.input_singles.is_of_type("fastq.gz"): |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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diff
changeset
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15 #set read1 = 'input_1.fastq.gz' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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16 #set compressed = 'gz' |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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17 #else |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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changeset
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18 #set read1 = 'input_1.fastq' |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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19 #end if |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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20 ln -s '${singlePaired.input_singles}' ${read1} && |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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21 #elif $singlePaired.sPaired == "paired": |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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22 #if $singlePaired.input_mate1.is_of_type("fastq.gz"): |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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23 #set read1 = 'input_1.fastq.gz' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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24 #set compressed = 'gz' |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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changeset
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25 #else |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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26 #set read1 = 'input_1.fastq' |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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changeset
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27 #end if |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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28 ln -s '${singlePaired.input_mate1}' ${read1} && |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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29 |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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30 #if $singlePaired.input_mate2.is_of_type("fastq.gz"): |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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31 #set read2 = 'input_2.fastq.gz' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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32 #else |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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diff
changeset
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33 #set read2 = 'input_2.fastq' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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34 #end if |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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35 ln -s '${singlePaired.input_mate2}' ${read2} && |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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36 #else: |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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37 #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"): |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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38 #set read1 = 'input_1.fastq.gz' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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39 #set compressed = 'gz' |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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changeset
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40 #else |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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41 #set read1 = 'input_1.fastq' |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
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42 #end if |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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43 ln -s '${singlePaired.input_mate_pairs.forward}' ${read1} && |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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44 |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
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45 #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"): |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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46 #set read2 = 'input_2.fastq.gz' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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47 #else |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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diff
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48 #set read2 = 'input_2.fastq' |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
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diff
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49 #end if |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
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50 ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} && |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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51 #end if |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
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52 |
11
80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
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53 trim_galore |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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54 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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55 ## according the develpers 4 cores could be a sweet spot, anything above has diminishing returns |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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56 --cores \${GALAXY_SLOTS:-4} |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
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57 |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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58 ## we only support fastqsanger |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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59 --phred33 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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60 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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61 #if $params.settingsType == "custom": |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
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62 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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63 ## default 20 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
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64 --quality $params.quality |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
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65 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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66 ## default 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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67 --stringency $params.stringency |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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68 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
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69 ## default 0.1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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70 -e $params.error_rate |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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71 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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72 ## default 20 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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73 --length $params.min_length |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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74 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
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75 #if $params.clip_R1: |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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76 --clip_R1 $params.clip_R1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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77 #end if |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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78 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
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79 #if $params.clip_R2: |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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80 --clip_R2 $params.clip_R2 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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81 #end if |
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82 |
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83 #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output": |
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84 --retain_unpaired |
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85 --length_1 $params.retain_unpaired.length_1 |
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86 --length_2 $params.retain_unpaired.length_2 |
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87 #end if |
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88 |
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89 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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90 |
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91 ## RBBS specific options. |
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92 #if $rrbs.settingsType == "custom": |
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93 $rrbs.rrbs |
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94 $rrbs.non_directional |
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95 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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96 |
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97 --output_dir ./ |
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98 |
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99 #if $params.settingsType == "custom" and not $params.report: |
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100 --no_report_file |
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101 #end if |
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102 |
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103 #if $singlePaired.trimming.trimming_select == 'user': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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104 ## default 'AGATCGGAAGAGC' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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105 #if $singlePaired.trimming.adapter.strip() != '': |
11
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106 --adapter '$singlePaired.trimming.adapter' |
6
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107 #end if |
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108 #else: |
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109 $singlePaired.trimming.trimming_select |
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110 #end if |
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111 |
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112 #if $singlePaired.three_prime_clip_R1: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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113 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1 |
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114 #end if |
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115 |
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116 #if $singlePaired.sPaired == "single": |
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117 ## input sequence |
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118 ${read1} |
6
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119 #else: |
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120 --paired |
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121 |
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122 $singlePaired.trim1 |
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123 |
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124 #if $singlePaired.trimming.trimming_select == 'user': |
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125 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '': |
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126 --adapter2 '$singlePaired.trimming.adapter2' |
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127 #end if |
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128 #end if |
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129 |
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130 #if $singlePaired.three_prime_clip_R2: |
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131 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2 |
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132 #end if |
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133 |
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134 ## input sequences |
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135 ${read1} |
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136 ${read2} |
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137 #end if |
6
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138 |
10
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139 #if $compressed == 'no': |
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140 --dont_gzip |
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141 #end if |
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142 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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143 ## Trimming settings |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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144 #if $trimming.settingsType == 'custom' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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145 #if $trimming.hardtrim5 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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146 --hardtrim5 $trimming.hardtrim5 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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147 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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148 #if $trimming.hardtrim3 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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149 --hardtrim3 $trimming.hardtrim3 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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150 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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151 $trimming.clock |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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152 $trimming.polyA |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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153 #end if |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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154 |
8
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155 ## Trim Galore is finished, rename the output if compressed |
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156 && |
10
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157 if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi |
8
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158 && |
10
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159 if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi |
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160 && |
10
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161 if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi |
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162 && |
10
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163 if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi |
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f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
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164 && |
10
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165 if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi |
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166 && |
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167 if [ -f input_1.clock_UMI.R1.fq.gz ] ; then mv input_1.clock_UMI.R1.fq.gz input_1.clock_UMI.R1.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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168 && |
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169 if [ -f input_2.clock_UMI.R2.fq.gz ] ; then mv input_2.clock_UMI.R2.fq.gz input_2.clock_UMI.R2.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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170 |
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171 ## Rename hardtrimmed files |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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172 #if $trimming.settingsType == 'custom' |
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173 && |
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174 if [ -f input_1.${trimming.hardtrim5}bp_5prime.fq.gz ] ; then mv input_1.${trimming.hardtrim5}bp_5prime.fq.gz input_1_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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175 && |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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176 if [ -f input_2.${trimming.hardtrim5}bp_5prime.fq.gz ] ; then mv input_2.${trimming.hardtrim5}bp_5prime.fq.gz input_2_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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177 && |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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178 if [ -f input_1.${trimming.hardtrim3}bp_3prime.fq.gz ] ; then mv input_1.${trimming.hardtrim3}bp_3prime.fq.gz input_1_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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179 && |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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180 if [ -f input_2.${trimming.hardtrim3}bp_3prime.fq.gz ] ; then mv input_2.${trimming.hardtrim3}bp_3prime.fq.gz input_2_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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181 && |
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182 if [ -f input_1.${trimming.hardtrim5}bp_5prime.fq ] ; then mv input_1.${trimming.hardtrim5}bp_5prime.fq input_1_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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183 && |
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184 if [ -f input_2.${trimming.hardtrim5}bp_5prime.fq ] ; then mv input_2.${trimming.hardtrim5}bp_5prime.fq input_2_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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185 && |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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186 if [ -f input_1.${trimming.hardtrim3}bp_3prime.fq ] ; then mv input_1.${trimming.hardtrim3}bp_3prime.fq input_1_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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187 && |
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188 if [ -f input_2.${trimming.hardtrim3}bp_3prime.fq ] ; then mv input_2.${trimming.hardtrim3}bp_3prime.fq input_2_hardtrim.fq ; fi |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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189 #end if |
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190 |
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191 ## Trim Galore! run is finished. Move the report files to the proper place |
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192 #if $params.settingsType == "custom" and $params.report: |
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193 && |
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194 cat ./*_trimming_report.txt > '$report_file' |
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195 #end if |
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196 && ls -lah |
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197 ]]></command> |
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198 <inputs> |
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199 <!-- Input Parameters --> |
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200 <conditional name="singlePaired"> |
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201 <param name="sPaired" type="select" label="Is this library paired- or single-end?"> |
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202 <option value="single">Single-end</option> |
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203 <option value="paired">Paired-end</option> |
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204 <option value="paired_collection">Paired Collection</option> |
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205 </param> |
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206 <when value="single"> |
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207 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" /> |
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208 <expand macro="adapter_trimming"/> |
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209 |
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210 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end"> |
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211 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed. |
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212 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. |
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213 (--three_prime_clip_R1)</help> |
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214 </param> |
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215 </when> |
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216 <when value="paired"> |
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217 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" /> |
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218 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" /> |
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219 <expand macro="paired_adapter_trimming" /> |
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220 </when> |
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221 <when value="paired_collection"> |
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222 <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" |
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223 label="Select a paired collection" help="See help section for an explanation of dataset collections"/> |
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224 <expand macro="paired_adapter_trimming" /> |
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225 </when> |
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226 </conditional> |
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227 |
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228 <conditional name="params"> |
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229 <param name="settingsType" type="select" label="Advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters."> |
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230 <option value="default">Use defaults</option> |
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231 <option value="custom">Full parameter list</option> |
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232 </param> |
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233 <when value="default" /> |
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234 <!-- Full/advanced params. --> |
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235 <when value="custom"> |
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236 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal (Enter phred quality score threshold)" |
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237 help="For more information please see below." /> |
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238 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" /> |
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239 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" /> |
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240 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" /> |
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241 |
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242 <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5' end of read 1" /> |
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243 <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5' end of read 2 (Only for paired-end reads)" /> |
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244 |
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245 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" /> |
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246 |
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247 <conditional name="retain_unpaired"> |
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248 <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads"> |
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249 <option value="no_output">Do not output unpaired reads</option> |
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250 <option value="retain_unpaired_output">Output unpaired reads</option> |
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251 </param> |
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252 <when value="no_output" /> |
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253 <!-- Output params. --> |
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254 <when value="retain_unpaired_output"> |
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255 <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" /> |
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256 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" /> |
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257 </when> <!-- output --> |
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258 </conditional> <!-- retain_unpaired --> |
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259 |
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260 </when> <!-- full --> |
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261 </conditional> <!-- params --> |
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262 |
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263 <conditional name="rrbs"> |
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264 <param name="settingsType" type="select" label="RRBS specific settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters."> |
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265 <option value="default">Use defaults (no RRBS)</option> |
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266 <option value="custom">Full parameter list</option> |
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267 </param> |
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268 <when value="default" /> |
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269 <!-- Full/advanced params. --> |
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270 <when value="custom"> |
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271 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True" |
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272 label="Specifies that the input file was an MspI digested RRBS sample" /> |
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273 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False" |
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274 label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" /> |
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275 </when> <!-- full --> |
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276 </conditional> <!-- params --> |
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277 <!--Trimming options--> |
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278 <conditional name="trimming"> |
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279 <param name="settingsType" type="select" label="Trimming settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters."> |
cd7e644cae1d
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280 <option value="default">Use defaults</option> |
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281 <option value="custom">Full parameter list</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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282 </param> |
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283 <when value="default" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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284 <when value="custom"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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285 <param argument="--hardtrim5" type="integer" min="1" optional="true" label="Hard-trimm 5' ends" help="Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 5'-end. Once hard-trimming of files is complete, it will exit" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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286 <param argument="--hardtrim3" type="integer" min="1" optional="true" label="Hard-trimm 3' ends" help="Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 3'-end. Once hard-trimming of files is complete, it will exit" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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287 <param argument="--clock" type="boolean" truevalue="--clock" falsevalue="" label="Mouse epigenetic clock mode" help="In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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288 <param argument="--polyA" type="boolean" truevalue="--polyA" falsevalue="" label="Remove polyA tails" help="This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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289 </when> |
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290 </conditional> |
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291 </inputs> |
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292 |
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293 <outputs> |
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294 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads"> |
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295 <filter>singlePaired['sPaired'] == "single"</filter> |
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296 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> |
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297 </data> |
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298 |
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299 <data format_source="input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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300 <filter>singlePaired['sPaired'] == "single"</filter> |
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301 <filter>trimming['settingsType'] == "custom"</filter> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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302 <filter>trimming['hardtrim3'] != '' or trimming['hardtrim5'] != ''</filter> |
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303 </data> |
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304 |
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305 <!--Trimmed reads paired collection--> |
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306 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads"> |
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307 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_val_1.fq" /> |
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308 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_val_2.fq" /> |
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309 <filter>singlePaired['sPaired'] == "paired_collection"</filter> |
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310 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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311 <filter>trimming['clock'] == False</filter> |
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312 </collection> |
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313 |
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314 <!--Unpaired reads collection--> |
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315 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads"> |
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316 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_unpaired_1.fq" /> |
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317 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_unpaired_2.fq" /> |
6
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318 <filter>params['settingsType'] == "custom"</filter> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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319 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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320 <filter>singlePaired['sPaired'] == "paired_collection"</filter> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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321 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> |
6
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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322 </collection> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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|
323 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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324 <!--Hard-trimmed reads paired collection--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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325 <collection name="hardtrimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: hard-trimmed paired reads"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
326 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_hardtrim.fq" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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327 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_hardtrim.fq" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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328 <filter>singlePaired['sPaired'] == "paired_collection"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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329 <filter>trimming['settingsType'] == "custom"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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330 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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331 </collection> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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332 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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333 <!--Mouse epigenetic reads paired collection--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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334 <collection name="mouse_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: MEC paired reads"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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335 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1.clock_UMI.R1.fq" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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336 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2.clock_UMI.R2.fq" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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337 <filter>singlePaired['sPaired'] == "paired_collection"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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338 <filter>trimming['settingsType'] == "custom"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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339 <filter>trimming['clock']</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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340 </collection> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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341 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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342 |
10
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343 <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq" |
6
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344 label="${tool.name} on ${on_string}: trimmed reads pair 1"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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345 <filter>singlePaired['sPaired'] == "paired"</filter> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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346 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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347 <filter>trimming['clock'] == False</filter> |
6
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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348 </data> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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349 |
10
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bgruening
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350 <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq" |
6
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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351 label="${tool.name} on ${on_string}: trimmed reads pair 2"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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352 <filter>singlePaired['sPaired'] == "paired"</filter> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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353 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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354 <filter>trimming['clock'] == False</filter> |
6
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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|
355 </data> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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|
356 |
10
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bgruening
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|
357 <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq" |
6
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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|
358 label="${tool.name} on ${on_string}: unpaired reads (1)"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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359 <filter>params['settingsType'] == "custom"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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360 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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361 <filter>singlePaired['sPaired'] == "paired"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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|
362 </data> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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|
363 |
10
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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|
364 <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq" |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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|
365 label="${tool.name} on ${on_string}: unpaired reads (2)"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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changeset
|
366 <filter>params['settingsType'] == "custom"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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changeset
|
367 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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368 <filter>singlePaired['sPaired'] == "paired"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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|
369 </data> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
370 <!--Hard-trimmed paired reads--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
371 <data format_source="input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_1_hardtrim.fq" |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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372 label="${tool.name} on ${on_string}: hard-trimmed reads pair 1"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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373 <filter>singlePaired['sPaired'] == "paired"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
374 <filter>trimming['settingsType'] == 'custom'</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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375 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
376 </data> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
377 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
378 <data format_source="input_mate2" name="hardtrimmed_reads_pair2" from_work_dir="input_2_hardtrim.fq" |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
379 label="${tool.name} on ${on_string}: hard-trimmed reads pair 2"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
380 <filter>singlePaired['sPaired'] == "paired"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
381 <filter>trimming['settingsType'] == 'custom'</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
382 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff
changeset
|
383 </data> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
384 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
385 <!--Mouse epigenetic mode paired reads--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
386 <data format_source="input_mate1" name="mec_reads_pair1" from_work_dir="input_1.clock_UMI.R1.fq" |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
387 label="${tool.name} on ${on_string}: MEC reads pair 1"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
388 <filter>singlePaired['sPaired'] == "paired"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
389 <filter>trimming['settingsType'] == 'custom'</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
390 <filter>trimming['clock']</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
391 </data> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
392 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
393 <data format_source="input_mate2" name="mec_reads_pair2" from_work_dir="input_2.clock_UMI.R2.fq" |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
394 label="${tool.name} on ${on_string}: MEC reads pair 2"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
395 <filter>singlePaired['sPaired'] == "paired"</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
396 <filter>trimming['settingsType'] == 'custom'</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
397 <filter>trimming['clock']</filter> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
398 </data> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
399 |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
400 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
401 <filter>params['settingsType'] == "custom"</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
402 <filter>params['report'] == True</filter> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
403 </data> |
11
80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents:
10
diff
changeset
|
404 </outputs> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
405 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
406 <tests> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
407 <test expect_num_outputs="2"> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
408 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
409 <param name="sPaired" value="single" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
410 <param name="settingsType" value="custom" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
411 <param name="report" value="true" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
412 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
413 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" /> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
414 </test> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
415 <test expect_num_outputs="2"> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
416 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
417 <param name="sPaired" value="single" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
418 <param name="settingsType" value="custom" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
419 <param name="report" value="true" /> |
14
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
420 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
421 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" /> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
422 </test> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
423 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
424 <test expect_num_outputs="1"> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
425 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
426 <param name="sPaired" value="single" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
427 <param name="trimming_select" value="--illumina" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
428 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
429 </test> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
430 <test expect_num_outputs="1"> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
431 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
432 <param name="sPaired" value="single" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
433 <param name="trimming_select" value="--illumina" /> |
14
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
434 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
435 </test> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
436 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
437 <test expect_num_outputs="1"> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
438 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
439 <param name="sPaired" value="single" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
440 <param name="adapter" value="AAAGAGC" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
441 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
442 </test> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
443 <test expect_num_outputs="1"> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
444 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
445 <param name="sPaired" value="single" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
446 <param name="adapter" value="AAAGAGC" /> |
14
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
447 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
448 </test> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
449 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
450 <test expect_num_outputs="3"> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
451 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
452 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
453 <param name="sPaired" value="paired" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
454 <param name="settingsType" value="custom" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
455 <param name="report" value="true" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
456 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
457 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/> |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
7
diff
changeset
|
458 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" /> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
459 </test> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
460 <test expect_num_outputs="3"> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
461 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
462 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
463 <param name="sPaired" value="paired" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
464 <param name="settingsType" value="custom" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
465 <param name="report" value="true" /> |
14
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
466 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
467 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
468 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
469 </test> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
470 |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
471 <test expect_num_outputs="7"> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
472 <param name="input_mate_pairs"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
473 <collection type="paired"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
474 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
475 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
476 </collection> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
477 </param> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
478 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
479 <param name="sPaired" value="paired_collection" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
480 <param name="settingsType" value="custom" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
481 <param name="report" value="true" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
482 <param name="retain_unpaired_select" value="retain_unpaired_output" /> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
483 |
8
f1e71aeaa923
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents:
7
diff
changeset
|
484 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" /> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
485 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
486 <output_collection name="trimmed_reads_paired_collection" type="paired"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
487 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
488 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
489 </output_collection> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
490 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
491 <output_collection name="trimmed_reads_unpaired_collection" type="paired"> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
492 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
493 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/> |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
494 </output_collection> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
495 </test> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
496 <test expect_num_outputs="7"> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
497 <param name="input_mate_pairs"> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
498 <collection type="paired"> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
499 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
500 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
501 </collection> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
502 </param> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
503 |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
504 <param name="sPaired" value="paired_collection" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
505 <param name="settingsType" value="custom" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
506 <param name="report" value="true" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
507 <param name="retain_unpaired_select" value="retain_unpaired_output" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
508 |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
509 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" /> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
510 |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
511 <output_collection name="trimmed_reads_paired_collection" type="paired"> |
14
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
512 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
513 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
514 </output_collection> |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
515 |
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
516 <output_collection name="trimmed_reads_unpaired_collection" type="paired"> |
14
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
517 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
949f01671246
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents:
13
diff
changeset
|
518 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents:
9
diff
changeset
|
519 </output_collection> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
520 </test> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
521 <!--Test hard-trim option--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
522 <test expect_num_outputs="2"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
523 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
524 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
525 <param name="sPaired" value="paired" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
526 <conditional name="trimming"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
527 <param name="settingsType" value="custom" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
528 <param name="hardtrim3" value="20"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
529 </conditional> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
530 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair1_.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
531 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
532 </test> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
533 <test expect_num_outputs="2"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
534 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
535 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
536 <param name="sPaired" value="paired" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
537 <conditional name="trimming"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
538 <param name="settingsType" value="custom" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
539 <param name="hardtrim5" value="20"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
540 </conditional> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
541 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair1_.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
542 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair2_.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
543 </test> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
544 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
545 <!--Test mouse epigenetic clock option--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
546 <test expect_num_outputs="2"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
547 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
548 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
549 <param name="sPaired" value="paired" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
550 <conditional name="trimming"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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551 <param name="settingsType" value="custom" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
552 <param name="clock" value="true"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
553 </conditional> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
554 <output name="mec_reads_pair1" file="mec_reads_pair1.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
555 <output name="mec_reads_pair2" file="mec_reads_pair2.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
556 </test> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
557 <!--Test polyA option--> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
558 <test expect_num_outputs="2"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
559 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
560 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
561 <param name="sPaired" value="paired" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
562 <conditional name="trimming"> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
563 <param name="settingsType" value="custom" /> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
564 <param name="polyA" value="true"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
565 </conditional> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
566 <output name="trimmed_reads_pair1" file="trimmed_polyA_reads_pair1.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
567 <output name="trimmed_reads_pair1" file="trimmed_polyA_reads_pair2.fastqsanger" ftype="fastqsanger"/> |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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568 </test> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
|
569 </tests> |
11
80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
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570 <help><![CDATA[ |
6
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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571 **What it does** |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
572 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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changeset
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573 `Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are: |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
574 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
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575 * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
576 * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
577 * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
578 * The Phred quality of basecalls and the stringency for adapter removal can be specified individually |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
579 * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
580 * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
581 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff
changeset
|
582 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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|
583 It is developed by Felix Krueger at the Babraham Institute. |
9
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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584 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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|
585 ---- |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
586 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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587 **Main Settings** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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588 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff
changeset
|
589 * **Adapter sequence to be trimmed** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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|
590 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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|
591 * **Automatic detection** |
11
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
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|
592 |
9
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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593 | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
594 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
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|
595 * **Illumina universal** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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|
596 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
597 | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
598 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
599 | *option --illumina* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
600 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
601 * **Nextera transposase** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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|
602 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
603 | Adapter sequence to be trimmed is the first 12bp of the Nextera adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
604 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
605 | *option --nextera* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
606 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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|
607 * **Illumina small RNA adapters** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
608 |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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|
609 | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5' adapter automatically ('GATCGTCGGACT') unless -a 2 had been defined explicitly. |
9
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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610 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
611 | *option --small_rna* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
612 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
613 * **User defined adapter trimming** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
614 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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changeset
|
615 | Adapter sequence to be trimmed is the sequence entered by the user instead of the default auto-detection of adapter sequence. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
616 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
617 | *option -a* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
618 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
619 * **If Single-End Reads** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
620 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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changeset
|
621 * **Remove <int> bp from the 3' end** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
622 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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changeset
|
623 | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
624 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
625 | *option --three_prime_clip_R1* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
626 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
changeset
|
627 * **If Paired-End Reads** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
628 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
629 * **Trims 1 bp off every read from its 3' end** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
630 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
631 | This may be needed for FastQ files that are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards alignments like this: |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
632 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
633 | R1 ---------------------------> |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
634 | R2 <--------------------------- |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
635 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
636 | or this: |
11
80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents:
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diff
changeset
|
637 | |
9
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
changeset
|
638 | R1 -----------------------> |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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changeset
|
639 | R2 <----------------- |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
640 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
changeset
|
641 | as invalid (whenever a start/end coordinate is contained within the other read). |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
642 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
643 | *option --t* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
644 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
645 * **Remove <int> bp from the 3' end of read 1** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
646 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
647 | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
648 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
649 | *option --three_prime_clip_R1* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
650 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
651 * **Remove <int> bp from the 3' end of read 2** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
652 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
653 | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
654 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
655 | *option --three_prime_clip_R2* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
656 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
657 ---- |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
658 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
659 **Advanced Settings** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
660 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
661 * **Trim low-quality ends from reads in addition to adapter removal** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
662 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
changeset
|
663 | For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract <INT> from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Default Phred score: 20. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
664 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
665 | *option -q* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
666 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
667 * **Overlap with adapter sequence required to trim a sequence** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
668 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
changeset
|
669 | Defaults to a very stringent setting of '1', i.e. even a single bp of overlapping sequence will be trimmed of the 3' end of any read. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
670 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
671 | *option -s* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
672 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff
changeset
|
673 * **Maximum allowed error rate** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
674 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
675 | (no. of errors divided by the length of the matching region) (default: 0.1). |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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changeset
|
676 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff
changeset
|
677 | *option -e* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
678 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
679 * **Discard reads that became shorter than length <INT>** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
680 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
changeset
|
681 | because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
682 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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changeset
|
683 | For paired-end files, both reads of a read-pair need to be longer than <INT> bp to be printed out to validated paired-end files (see option --paired). If only one read became too short there is the possibility of keeping such unpaired single-end reads (see --retain_unpaired). Default pair-cutoff: 20 bp. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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diff
changeset
|
684 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
685 | *option --length* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
686 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
687 * **Instructs Trim Galore! to remove INT bp from the 5' end of read 1** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
688 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
689 | Instructs Trim Galore to remove <INT> bp from the 5' end of read 1 (or single-end reads). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. Default: OFF. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
690 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
691 | *option --clip_R1* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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changeset
|
692 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
693 * **Instructs Trim Galore! to remove INT bp from the 5' end of read 2** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
694 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
695 | Instructs Trim Galore to remove <int> bp from the 5' end of read 2 (paired-end reads only). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. For paired-end BS-Seq, it is recommended to remove the first few bp because the end-repair reaction may introduce a bias towards low methylation. Please refer to the M-bias plot section in the Bismark User Guide for some examples. Default: OFF. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff
changeset
|
696 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
697 | *option --clip_R2* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
698 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
699 * **Specify if you would like to retain unpaired reads** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff
changeset
|
700 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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changeset
|
701 | If only one of the two paired-end reads became too short, the longer read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output files. The length cutoff for unpaired single-end reads is governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
702 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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|
703 | *option --retained_unpaired* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff
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|
704 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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|
705 ---- |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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|
706 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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changeset
|
707 **RRBS specific settings** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
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|
708 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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parents:
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diff
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|
709 * **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
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|
710 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
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|
711 | Sequences which were adapter-trimmed will have a further 2 bp removed from their 3' end. This is to avoid that the filled-in C close to the second MspI site in a sequence is used for methylation calls. Sequences which were merely trimmed because of poor quality will not be shortened further. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
8
diff
changeset
|
712 | |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
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|
713 | *option -rrbs* |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
8
diff
changeset
|
714 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
changeset
|
715 * **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs** |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
8
diff
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|
716 |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
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diff
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|
717 | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well. |
1bfc7254232e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents:
8
diff
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|
718 | |
11
80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents:
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diff
changeset
|
719 | *option --non_directional* |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
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|
720 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
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|
721 ---- |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
722 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
723 **Trim specific seetings** |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
724 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
725 * **Hard-trimming mode** |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
726 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
727 | Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 5' or 3' -end. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
728 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
729 | *options -hardtrim5 and -hardtrim3* |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
730 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
731 * **Mouse Epigenetic Clock mode** |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
732 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
733 | In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock (see here: `Multi-tissue DNA methylation age predictor in mouse`_). Following this, Trim Galore will exit. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
734 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
735 | In it's current implementation, the dual-UMI RRBS reads come in the following format: |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
736 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
737 | Read 1 5' UUUUUUUU CAGTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TACTG UUUUUUUU 3' |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
738 | Read 2 3' UUUUUUUU GTCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF ATGAC UUUUUUUU 5' |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
739 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
740 | Where UUUUUUUU is a random 8-mer unique molecular identifier (UMI), CAGTA is a constant region, and FFFFFFF... is the actual RRBS-Fragment to be sequenced. The UMIs for Read 1 (R1) and Read 2 (R2), as well as the fixed sequences (F1 or F2), are written into the read ID and removed from the actual sequence. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
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|
741 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
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|
742 | *option --clock* |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
743 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
changeset
|
744 * **PolyA mode** |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
745 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
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|
746 | This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences. When selected, Trim Galore attempts to identify from the first supplied sample whether sequences contain more often a stretch of either 'AAAAAAAAAA' or 'TTTTTTTTTT'. This determines if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary base from the start of the reads. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
747 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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parents:
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diff
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|
748 | PLEASE NOTE: The poly-A trimming mode expects that sequences were both adapter and quality trimmed before looking for Poly-A tails, and it is the user's responsibility to carry out an initial round of trimming. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
749 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
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|
750 | *option --polyA* |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
751 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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changeset
|
752 * **Amplicon mode** |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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changeset
|
753 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
754 | This is a special mode of operation for paired-end data, such as required for the IMPLICON method, where a UMI sequence is getting transferred from the start of Read 2 to the readID of both reads. Following this, Trim Galore will exit. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
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|
755 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
changeset
|
756 | In it's current implementation, the UMI carrying reads come in the following format: |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
15
diff
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|
757 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
758 | Read 1 5' FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 3' |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
759 | Read 2 3' UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5' |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
760 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
761 | Where UUUUUUUU is a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual fragment to be sequenced. |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff
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|
762 | |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
763 | *option --amplicon* |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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diff
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|
764 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
765 .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
766 .. _Multi-tissue DNA methylation age predictor in mouse: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1203-5 |
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents:
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|
767 |
11
80cd83b11214
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
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|
768 ]]></help> |
16
cd7e644cae1d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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|
769 <expand macro="citations" /> |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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770 </tool> |