Mercurial > repos > bgruening > trim_galore

annotate trim_galore.xml @ 15:084bbd8ba7b8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
author bgruening
date Tue, 30 Jul 2019 06:26:49 -0400
parents 949f01671246
children cd7e644cae1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
084bbd8ba7b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
parents: 14
diff changeset
1 <tool id="trim_galore" name="Trim Galore!" version="0.6.3" profile="17.01">
084bbd8ba7b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
parents: 14
diff changeset
2 <!-- Wrapper compatible with Trim Galore! version 0.6.3 -->
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
3 <description>Quality and adapter trimmer of reads</description>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
4 <macros>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
5 <macro name="adapter_trimming">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
6 <conditional name="trimming">
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
7 <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
8 <option value="">Automatic detection</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
9 <option value="--illumina">Illumina universal</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
10 <option value="--nextera">Nextera transposase</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
11 <option value="--small_rna">Illumina small RNA adapters</option>
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
12 <option value="user">User defined adapter sequence</option>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
13 </param>
7
8352713cf939 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 07148c518916e16602ea26473d00358fe04bc3b6-dirty
bgruening
parents: 6
diff changeset
14 <when value=""/>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
15 <when value="--illumina"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
16 <when value="--nextera"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
17 <when value="--small_rna"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
18 <when value="user">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
19 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
20 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
21 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
22 <yield/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
23 </when>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
24 </conditional>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
25 </macro>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
26 <macro name="paired_adapter_trimming">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
27 <expand macro="adapter_trimming">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
28 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
29 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
30 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
31 </expand>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
32 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
33 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
34 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
35 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
36 (--three_prime_clip_R1)</help>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
37 </param>
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
38 <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
39 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
40 adapter/quality trimming has been performed. This may remove some unwanted bias from
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
41 the 3' end that is not directly related to adapter sequence or basecall quality.</help>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
42 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
43 </macro>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
44 </macros>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
45 <requirements>
15
084bbd8ba7b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
parents: 14
diff changeset
46 <requirement type="package" version="0.6.3">trim-galore</requirement>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
47 </requirements>
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
48 <version_command>
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
49 trim_galore --version
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
50 </version_command>
13
b6c00b82f623 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit be11349529528f508eb05073396e80c3d1cbed4d
bgruening
parents: 12
diff changeset
51 <command detect_errors="aggressive"><![CDATA[
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
52 #set compressed = 'no'
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
53 #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
54 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
55 #set read1 = 'input_1.fastq.gz'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
56 #set compressed = 'gz'
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
57 #else
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
58 #set read1 = 'input_1.fastq'
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
59 #end if
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
60 ln -s '${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
61 #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
62 #if $singlePaired.input_mate1.is_of_type("fastq.gz"):
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
63 #set read1 = 'input_1.fastq.gz'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
64 #set compressed = 'gz'
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
65 #else
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
66 #set read1 = 'input_1.fastq'
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
67 #end if
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
68 ln -s '${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
69
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
70 #if $singlePaired.input_mate2.is_of_type("fastq.gz"):
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
71 #set read2 = 'input_2.fastq.gz'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
72 #else
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
73 #set read2 = 'input_2.fastq'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
74 #end if
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
75 ln -s '${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
76 #else:
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
77 #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
78 #set read1 = 'input_1.fastq.gz'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
79 #set compressed = 'gz'
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
80 #else
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
81 #set read1 = 'input_1.fastq'
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
82 #end if
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
83 ln -s '${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
84
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
85 #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
86 #set read2 = 'input_2.fastq.gz'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
87 #else
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
88 #set read2 = 'input_2.fastq'
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
89 #end if
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
90 ln -s '${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
91 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
92
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
93 trim_galore
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
94
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
95 ## we only support fastqsanger
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
96 --phred33
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
97
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
98 #if $params.settingsType == "custom":
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
99
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
100 ## default 20
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
101 --quality $params.quality
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
102
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
103 ## default 1
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
104 --stringency $params.stringency
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
105
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
106 ## default 0.1
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
107 -e $params.error_rate
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
108
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
109 ## default 20
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
110 --length $params.min_length
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
111
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
112 #if $params.clip_R1:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
113 --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:
diff changeset
114 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
115
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
116 #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
117 --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:
diff changeset
118 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
119
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
120 #if $params.retain_unpaired.retain_unpaired_select == "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
121 --retain_unpaired
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
122 --length_1 $params.retain_unpaired.length_1
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
123 --length_2 $params.retain_unpaired.length_2
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
124 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
125
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
126 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
127
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
128 ## RBBS specific options.
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
129 #if $rrbs.settingsType == "custom":
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
130 $rrbs.rrbs
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
131 $rrbs.non_directional
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
132 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
133
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
134 --output_dir ./
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
135
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
136 #if $params.settingsType == "custom" and not $params.report:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
137 --no_report_file
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
138 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
139
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
140 #if $singlePaired.trimming.trimming_select == 'user':
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
141 ## default 'AGATCGGAAGAGC'
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
142 #if $singlePaired.trimming.adapter.strip() != '':
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
143 --adapter '$singlePaired.trimming.adapter'
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
144 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
145 #else:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
146 $singlePaired.trimming.trimming_select
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
147 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
148
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
149 #if $singlePaired.three_prime_clip_R1:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
150 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
151 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
152
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
153 #if $singlePaired.sPaired == "single":
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
154 ## input sequence
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
155 ${read1}
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
156 #else:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
157 --paired
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
158
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
159 $singlePaired.trim1
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
160
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
161 #if $singlePaired.trimming.trimming_select == 'user':
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
162 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
163 --adapter2 '$singlePaired.trimming.adapter2'
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
164 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
165 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
166
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
167 #if $singlePaired.three_prime_clip_R2:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
168 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
169 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
170
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
171 ## input sequences
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
172 ${read1}
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
173 ${read2}
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
174 #end if
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
175
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
176 #if $compressed == 'no':
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
177 --dont_gzip
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
178 #end if
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
179
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
180 ## Trim Galore is finished, rename the output if compressed
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
181 &&
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
182 if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
183 &&
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
184 if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
185 &&
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
186 if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
187 &&
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
188 if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
189 &&
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
190 if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
191
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
192 ## Trim Galore! run is finished. Move the report files to the proper place
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
193 #if $params.settingsType == "custom" and $params.report:
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
194 &&
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
195 cat ./*_trimming_report.txt > '$report_file'
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
196 #end if
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
197 ]]></command>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
198 <inputs>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
199 <!-- Input Parameters -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
200 <conditional name="singlePaired">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
201 <param name="sPaired" type="select" label="Is this library paired- or single-end?">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
202 <option value="single">Single-end</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
203 <option value="paired">Paired-end</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
204 <option value="paired_collection">Paired Collection</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
205 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
206 <when value="single">
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
207 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
208 <expand macro="adapter_trimming"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
209
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
210 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
211 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
212 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
213 (--three_prime_clip_R1)</help>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
214 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
215 </when>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
216 <when value="paired">
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
217 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
218 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
219 <expand macro="paired_adapter_trimming" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
220 </when>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
221 <when value="paired_collection">
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
222 <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
223 label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
224 <expand macro="paired_adapter_trimming" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
225 </when>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
226 </conditional>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
227
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
228 <conditional name="params">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
229 <param name="settingsType" type="select" label="Trim Galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
230 <option value="default">Use defaults</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
231 <option value="custom">Full parameter list</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
232 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
233 <when value="default" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
234 <!-- Full/advanced params. -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
235 <when value="custom">
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
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)"
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
237 help="For more information please see below." />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
238 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
239 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
240 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
241
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
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" />
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
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)" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
244
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
245 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
246
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
247 <conditional name="retain_unpaired">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
248 <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
249 <option value="no_output">Do not output unpaired reads</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
250 <option value="retain_unpaired_output">Output unpaired reads</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
251 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
252 <when value="no_output" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
253 <!-- Output params. -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
254 <when 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
255 <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
256 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
257 </when> <!-- output -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
258 </conditional> <!-- retain_unpaired -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
259
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
260 </when> <!-- full -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
261 </conditional> <!-- params -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
262
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
263 <conditional name="rrbs">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
264 <param name="settingsType" type="select" label="RRBS specific settings">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
265 <option value="default">Use defaults (no RRBS)</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
266 <option value="custom">Full parameter list</option>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
267 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
268 <when value="default" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
269 <!-- Full/advanced params. -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
270 <when value="custom">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
271 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
272 label="Specifies that the input file was an MspI digested RRBS sample" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
273 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
274 label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
275 </when> <!-- full -->
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
276 </conditional> <!-- params -->
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
277 </inputs>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
278
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
279 <outputs>
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
280 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
281 <filter>singlePaired['sPaired'] == "single"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
282 </data>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
283
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
284 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
285 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_val_1.fq" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
286 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_val_2.fq" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
287 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
288 </collection>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
289
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
290 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
291 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_unpaired_1.fq" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
292 <data name="reverse" format_source="input_mate_pairs['forward']" 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
parents:
diff changeset
293 <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
294 <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
parents:
diff changeset
295 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
296 </collection>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
297
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
298 <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
299 label="${tool.name} on ${on_string}: trimmed reads pair 1">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
300 <filter>singlePaired['sPaired'] == "paired"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
301 </data>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
302
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
303 <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
304 label="${tool.name} on ${on_string}: trimmed reads pair 2">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
305 <filter>singlePaired['sPaired'] == "paired"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
306 </data>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
307
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
308 <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
309 label="${tool.name} on ${on_string}: unpaired reads (1)">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
310 <filter>params['settingsType'] == "custom"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
311 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
312 <filter>singlePaired['sPaired'] == "paired"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
313 </data>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
314
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
315 <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
316 label="${tool.name} on ${on_string}: unpaired reads (2)">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
317 <filter>params['settingsType'] == "custom"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
318 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
319 <filter>singlePaired['sPaired'] == "paired"</filter>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
320 </data>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
321 <data format="txt" name="report_file" label="${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
322 <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
323 <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
324 </data>
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
325 </outputs>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
326
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
327 <tests>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
328 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
329 <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
330 <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
331 <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
332 <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
333 <output name="trimmed_reads_single" file="sanger_full_range_results1.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
334 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="8" />
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
335 </test>
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
336 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
337 <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
338 <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
339 <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
340 <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
341 <output name="trimmed_reads_single" file="sanger_full_range_results1.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
342 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
343 </test>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
344
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
345 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
346 <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
347 <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
348 <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
349 <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
350 </test>
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
351 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
352 <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
353 <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
354 <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
355 <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
356 </test>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
357
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
358 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
359 <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
360 <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
361 <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
362 <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
363 </test>
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
364 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
365 <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
366 <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
367 <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
368 <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
369 </test>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
370
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
371 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
372 <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
373 <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
374 <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
375 <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
376 <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
377 <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
378 <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
379 <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
380 </test>
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
381 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
382 <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
383 <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
384 <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
385 <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
386 <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
387 <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
388 <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
389 <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
390 </test>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
391
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
392 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
393 <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
394 <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
395 <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
396 <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
397 </collection>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
398 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
399
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
400 <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
401 <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
402 <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
403 <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
404
8
f1e71aeaa923 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 7
diff changeset
405 <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
406
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
407 <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
408 <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
409 <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
410 </output_collection>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
411
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
412 <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
413 <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
414 <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
415 </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
416 </test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
417 <test>
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="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
419 <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
420 <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
421 <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
422 </collection>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
423 </param>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
424
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
425 <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
426 <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
427 <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
428 <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
429
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
430 <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
431
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
432 <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
433 <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
434 <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
435 </output_collection>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
436
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
437 <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
438 <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
439 <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
440 </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
441 </test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
442 </tests>
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
443 <help><![CDATA[
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
444 **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
445
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
446 `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
447
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
448 * 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
449 * 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
450 * 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
451 * 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
452 * 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
453 * 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
454
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
455 .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
456
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
457 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
bgruening
parents: 8
diff changeset
458
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
459 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
460
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
461 **Main Settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
462
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
463 * **Adapter sequence to be trimmed**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
464
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
465 * **Automatic detection**
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
466
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
467 | 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
bgruening
parents: 8
diff changeset
468
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
469 * **Illumina universal**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
470
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
471 | 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
bgruening
parents: 8
diff changeset
472 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
473 | *option --illumina*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
474
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
475 * **Nextera transposase**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
476
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
477 | 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
bgruening
parents: 8
diff changeset
478 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
479 | *option --nextera*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
480
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
481 * **Illumina small RNA adapters**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
482
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
483 | 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
bgruening
parents: 8
diff changeset
484 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
485 | *option --small_rna*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
486
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
487 * **User defined adapter trimming**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
488
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
489 | 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
bgruening
parents: 8
diff changeset
490 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
491 | *option -a*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
492
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
493 * **If Single-End Reads**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
494
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
495 * **Remove <int> bp from the 3' end**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
496
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
497 | <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: 8
diff changeset
498 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
499 | *option --three_prime_clip_R1*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
500
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
501 * **If Paired-End Reads**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
502
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
503 * **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: 8
diff changeset
504
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
505 | 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: 8
diff changeset
506 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
507 | R1 --------------------------->
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
508 | R2 <---------------------------
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
509 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
510 | or this:
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
511 |
9
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
512 | R1 ----------------------->
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
513 | R2 <-----------------
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
514 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
515 | 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: 8
diff changeset
516 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
517 | *option --t*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
518
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
519 * **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: 8
diff changeset
520
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
521 | <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: 8
diff changeset
522 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
523 | *option --three_prime_clip_R1*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
524
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
525 * **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: 8
diff changeset
526
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
527 | <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: 8
diff changeset
528 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
529 | *option --three_prime_clip_R2*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
530
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
531 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
532
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
533 **Advanced Settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
534
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
535 * **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: 8
diff changeset
536
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
537 | 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: 8
diff changeset
538 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
539 | *option -q*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
540
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
541 * **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: 8
diff changeset
542
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
543 | 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: 8
diff changeset
544 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
545 | *option -s*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
546
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
547 * **Maximum allowed error rate**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
548
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
549 | (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
bgruening
parents: 8
diff changeset
550 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
551 | *option -e*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
552
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
553 * **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
bgruening
parents: 8
diff changeset
554
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
555 | 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
bgruening
parents: 8
diff changeset
556 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
557 | 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
bgruening
parents: 8
diff changeset
558 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
559 | *option --length*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
560
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
561 * **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: 8
diff changeset
562
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
563 | 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: 8
diff changeset
564 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
565 | *option --clip_R1*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
566
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
567 * **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: 8
diff changeset
568
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
569 | 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
parents: 8
diff changeset
570 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
571 | *option --clip_R2*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
572
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
573 * **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
parents: 8
diff changeset
574
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
575 | 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: 8
diff changeset
576 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
577 | *option --retained_unpaired*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
578
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
579 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
580
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
581 **RRBS specific settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
582
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
583 * **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: 8
diff changeset
584
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
585 | 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
586 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
587 | *option -rrbs*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
588
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
589 * **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 changeset
590
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
591 | 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 changeset
592 |
11
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
593 | *option --non_directional*
80cd83b11214 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
594 ]]></help>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
595 <citations></citations>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
596 </tool>