Mercurial > repos > pjbriggs > trimmomatic

annotate trimmomatic.xml @ 13:898b67846b47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated to Trimmomatic 0.38.
author pjbriggs
date Mon, 08 Jul 2019 07:09:10 -0400
parents 59054f086eca
children d94aff5ee623
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
898b67846b47 Updated to Trimmomatic 0.38.
pjbriggs
parents: 11
diff changeset
1 <tool id="trimmomatic" name="Trimmomatic" version="0.38.0">
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
2 <description>flexible read trimming tool for Illumina NGS data</description>
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
3 <macros>
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
4 <import>trimmomatic_macros.xml</import>
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
5 </macros>
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
6 <requirements>
13
898b67846b47 Updated to Trimmomatic 0.38.
pjbriggs
parents: 11
diff changeset
7 <requirement type="package" version="0.38">trimmomatic</requirement>
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
8 </requirements>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
10 @CONDA_TRIMMOMATIC_JAR_PATH@ &&
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
11 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
12 #if $readtype.single_or_paired == "pair_of_files"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
13 #set r1_ext = $readtype.fastq_r1_in.extension
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
14 #set r2_ext = $readtype.fastq_r2_in.extension
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
15 ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
16 ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
17 #elif $readtype.single_or_paired == "collection"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
18 #set r1_ext = $readtype.fastq_pair.forward.extension
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
19 #set r2_ext = $readtype.fastq_pair.reverse.extension
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
20 ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
21 ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
22 #else
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
23 ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
24 #end if
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
25 java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
26 #if $readtype.single_or_paired in ["pair_of_files","collection"]
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
27 PE -threads \${GALAXY_SLOTS:-6}
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
28 fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
29 fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
30 fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
31 #else
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
32 SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
33 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
34 ## ILLUMINACLIP option
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
35 #if $illuminaclip.do_illuminaclip
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
36 #if $illuminaclip.adapter_type.standard_or_custom == "custom"
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
37 #if $readtype.single_or_paired in ["pair_of_files","collection"]
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
38 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
39 #else
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
40 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
41 #end if
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
42 #else
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
43 #if $readtype.single_or_paired in ["pair_of_files","collection"]
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
44 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
45 #else
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
46 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
47 #end if
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
48 #end if
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
49 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
50 ## Other operations
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
51 #for $op in $operations
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
52 ## SLIDINGWINDOW
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
53 #if str( $op.operation.name ) == "SLIDINGWINDOW"
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
54 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
55 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
56 ## MINLEN:36
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
57 #if str( $op.operation.name ) == "MINLEN"
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
58 MINLEN:$op.operation.minlen
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
59 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
60 #if str( $op.operation.name ) == "LEADING"
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
61 LEADING:$op.operation.leading
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
62 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
63 #if str( $op.operation.name ) == "TRAILING"
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
64 TRAILING:$op.operation.trailing
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
65 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
66 #if str( $op.operation.name ) == "CROP"
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
67 CROP:$op.operation.crop
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
68 #end if
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
69 #if str( $op.operation.name ) == "HEADCROP"
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
70 HEADCROP:$op.operation.headcrop
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
71 #end if
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
72 #if str( $op.operation.name ) == "AVGQUAL"
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
73 AVGQUAL:$op.operation.avgqual
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
74 #end if
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
75 #if str( $op.operation.name ) == "MAXINFO"
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
76 MAXINFO:$op.operation.target_length:$op.operation.strictness
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
77 #end if
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
78 #end for
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
79 #if $output_logs:
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
80 -trimlog trimlog
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
81 #end if
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
82 2>&1 | tee trimmomatic.log &&
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
83 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
84 &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
85 #if $readtype.single_or_paired == "pair_of_files"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
86 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
87 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
88 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
89 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
90 #elif $readtype.single_or_paired == "collection"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
91 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
92 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
93 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
94 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
95 #else
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
96 mv fastq_out.'$fastq_in.extension' '${fastq_out}'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
97 #end if
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
98 ]]></command>
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
99 <configfiles>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
100 <configfile name="adapter_file_from_text">#set from_text_area = ''
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
101 #if str( $illuminaclip.do_illuminaclip ) == "yes" and str( $illuminaclip.adapter_type.standard_or_custom ) == "custom":
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
102 #set from_text_area = $illuminaclip.adapter_type.adapter_text
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
103 #end if
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
104 ${from_text_area}</configfile>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
105 </configfiles>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
106
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
107 <inputs>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
108 <conditional name="readtype">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
109 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
110 <option value="se" selected="true">Single-end</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
111 <option value="pair_of_files">Paired-end (two separate input files)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
112 <option value="collection">Paired-end (as collection)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
113 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
114 <when value="se">
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
115 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
116 </when>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
117 <when value="pair_of_files">
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
118 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
119 label="Input FASTQ file (R1/first of pair)" />
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
120 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
121 label="Input FASTQ file (R2/second of pair)" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
122 </when>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
123 <when value="collection">
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
124 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
125 </when>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
126 </conditional>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
127 <conditional name="illuminaclip">
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
128 <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="False" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
129 <when value="yes">
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
130 <conditional name="adapter_type">
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
131 <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?">
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
132 <option value="standard" selected="true">Standard</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
133 <option value="custom">Custom</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
134 </param>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
135 <when value="standard">
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
136 <param name="adapter_fasta" type="select" label="Adapter sequences to use">
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
137 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
138 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
139 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
140 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
141 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
142 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
143 </param>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
144 </when>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
145 <when value="custom">
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
146 <param name="adapter_text" type="text" area="True" size="10x30" value=""
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
147 label="Custom adapter sequences in fasta format" help="Write sequences in the fasta format.">
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
148 <sanitizer>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
149 <valid initial="string.printable"></valid>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
150 <mapping initial="none"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
151 </sanitizer>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
152 </param>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
153 </when>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
154 </conditional>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
155 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
156 <param name="palindrome_clip_threshold" type="integer" label="How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment" value="30" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
157 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
158 <param name="min_adapter_len" type="integer" label="Minimum length of adapter that needs to be detected (PE specific/palindrome mode)" value="8" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
159 <param name="keep_both_reads" type="boolean" label="Always keep both reads (PE specific/palindrome mode)?" truevalue="true" falsevalue="false" checked="true"
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
160 help="See help below"/>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
161 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
162 <when value="no" /> <!-- empty clause to satisfy planemo lint -->
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
163 </conditional>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
164 <repeat name="operations" title="Trimmomatic Operation" min="1">
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
165 <conditional name="operation">
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
166 <param name="name" type="select" label="Select Trimmomatic operation to perform">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
167 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
168 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
169 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
170 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
171 <option value="CROP">Cut the read to a specified length (CROP)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
172 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
173 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
174 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
175 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
176 <when value="SLIDINGWINDOW">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
177 <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
178 <param name="required_quality" type="integer" label="Average quality required" value="20" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
179 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
180 <when value="MINLEN">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
181 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
182 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
183 <when value="LEADING">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
184 <param name="leading" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the start of the read with quality below the threshold will be removed" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
185 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
186 <when value="TRAILING">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
187 <param name="trailing" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the end of the read with quality below the threshold will be removed" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
188 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
189 <when value="CROP">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
190 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
191 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
192 <when value="HEADCROP">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
193 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
194 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
195 <when value="AVGQUAL">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
196 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
197 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
198 <when value="MAXINFO">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
199 <param name="target_length" type="integer" label="Target read length" value="" help="The read length which is likely to allow the location of the read within the target sequence to be determined." />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
200 <param name="strictness" type="float" label="Strictness" value="" help="Set between zero and one - specifies the balance between preserving read length versus removal of incorrect bases; low values (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
201 </when>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
202 </conditional>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
203 </repeat>
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
204 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
205 <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
206 </inputs>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
207 <outputs>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
208 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
209 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
210 </data>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
211 <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
212 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
213 </data>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
214 <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
215 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
216 </data>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
217 <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
218 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
219 </data>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
220 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
221 <filter>readtype['single_or_paired'] == 'se'</filter>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
222 </data>
7
6eeacf19a38e Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents: 6
diff changeset
223 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
224 <filter>readtype['single_or_paired'] == "collection"</filter>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
225 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
226 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
227 </collection>
7
6eeacf19a38e Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
pjbriggs
parents: 6
diff changeset
228 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
229 <filter>readtype['single_or_paired'] == "collection"</filter>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
230 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
231 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
232 </collection>
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
233 <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
234 <filter>output_logs</filter>
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
235 </data>
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
236 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
237 <filter>output_err</filter>
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
238 </data>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
239 </outputs>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
240 <tests>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
241 <test>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
242 <!-- Single-end example -->
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
243 <conditional name="readtype">
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
244 <param name="single_or_paired" value="se" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
245 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
246 </conditional>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
247 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
248 <param name="output_logs" value="yes" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
249 <param name="output_err" value="yes" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
250 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
251 <output name="log_file" file="trimmomatic_se_out1.log" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
252 <output name="err_file" file="trimmomatic_se_out1.err" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
253 </test>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
254 <test>
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
255 <!-- Single-end example - gzipped -->
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
256 <param name="single_or_paired" value="se" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
257 <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
258 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
259 <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
260 </test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
261 <test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
262 <!-- Paired-end example - gzipped -->
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
263 <param name="single_or_paired" value="pair_of_files" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
264 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
265 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
266 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
267 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
268 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
269 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
270 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
271 </test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
272 <test>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
273 <!-- Paired-end example -->
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
274 <param name="single_or_paired" value="pair_of_files" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
275 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
276 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
277 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
278 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
279 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
280 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
281 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
282 </test>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
283 <test>
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
284 <!-- Paired-end Illumina 1.3-1.7 quality encoding -->
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
285 <param name="single_or_paired" value="pair_of_files" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
286 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
287 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
288 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
289 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
290 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
291 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
292 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
293 </test>
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
294 <test>
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
295 <!-- Paired-end Solexa quality encoding -->
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
296 <param name="single_or_paired" value="pair_of_files" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
297 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
298 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
299 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
300 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
301 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
302 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
303 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" />
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
304 </test>
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
305 <test>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
306 <!-- Single-end example (cropping) -->
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
307 <param name="single_or_paired" value="se" />
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
308 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
309 <param name="operations_0|operation|name" value="CROP" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
310 <param name="operations_0|operation|crop" value="10" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
311 <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
312 </test>
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
313 <test>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
314 <!-- Paired-end with dataset collection -->
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
315 <param name="single_or_paired" value="collection" />
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
316 <param name="fastq_pair">
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
317 <collection type="paired">
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
318 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
319 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
320 </collection>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
321 </param>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
322 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
323 <output_collection name="fastq_out_paired" type="paired">
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
324 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
325 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
326 </output_collection>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
327 <output_collection name="fastq_out_unpaired" type="paired">
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
328 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
329 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
330 </output_collection>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
331 </test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
332 <test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
333 <!-- Paired-end with dataset collection - gzipped -->
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
334 <param name="single_or_paired" value="collection" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
335 <param name="fastq_pair">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
336 <collection type="paired">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
337 <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
338 <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
339 </collection>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
340 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
341 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
342 <output_collection name="fastq_out_paired" type="paired">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
343 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
344 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
345 </output_collection>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
346 <output_collection name="fastq_out_unpaired" type="paired">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
347 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
348 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
349 </output_collection>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
350 </test>
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
351 <test>
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
352 <!-- Single-end using AVGQUAL -->
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
353 <param name="single_or_paired" value="se" />
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
354 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
355 <param name="operations_0|operation|name" value="AVGQUAL" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
356 <param name="operations_0|operation|avgqual" value="30" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
357 <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
358 </test>
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
359 <test>
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
360 <!-- Single-end using MAXINFO -->
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
361 <param name="single_or_paired" value="se" />
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
362 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
363 <param name="operations_0|operation|name" value="MAXINFO" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
364 <param name="operations_0|operation|target_length" value="75" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
365 <param name="operations_0|operation|strictness" value="0.8" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
366 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
367 </test>
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
368 <test>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
369 <!-- Paired-end ILLUMINACLIP - this does not check valid clipping -->
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
370 <param name="single_or_paired" value="pair_of_files" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
371 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
372 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
373 <param name="do_illuminaclip" value="true"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
374 <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
375 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
376 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
377 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
378 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
379 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
380 </test>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
381 <test>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
382 <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping -->
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
383 <param name="single_or_paired" value="pair_of_files" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
384 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
385 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
386 <param name="do_illuminaclip" value="true"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
387 <param name="standard_or_custom" value="custom"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
388 <param name="adapter_text"
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
389 value=">PrefixPE/1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PrefixPE/2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PCR_Primer1_rc&#10;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT&#10;>PCR_Primer2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer2_rc&#10;AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG&#10;>FlowCell1&#10;TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC&#10;>FlowCell2&#10;TTTTTTTTTTCAAGCAGAAGACGGCATACGA&#10;"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
390 <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
391 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
392 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
393 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
394 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
395 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
396 </test>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
397 </tests>
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
398 <help><![CDATA[
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
399 .. class:: infomark
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
400
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
401 **What it does**
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
402
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
403 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
404 single ended data.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
405
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
406 This tool allows the following trimming steps to be performed:
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
407
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
408 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
409
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
410 * If **Always keep both reads (PE specific/palindrome mode)** is True, the reverse read will also be retained in palindrome mode.
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
411 After read-though has been detected by palindrome mode, and the adapter sequence removed,
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
412 the reverse read contains the same sequence information as the forward read, albeit in reverse complement.
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
413 For this reason, the default behaviour is to entirely drop the reverse read.
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
414 Retaining the reverse read may be useful e.g. if the downstream tools cannot handle a combination of paired and unpaired reads.
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
415 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
416 quality within the window falls below a threshold
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
417 * **MINLEN:** Drop the read if it is below a specified length
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
418 * **LEADING:** Cut bases off the start of a read, if below a threshold quality
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
419 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
420 * **CROP:** Cut the read to a specified length
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
421 * **HEADCROP:** Cut the specified number of bases from the start of the read
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
422 * **AVGQUAL:** Drop the read if the average quality is below a specified value
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
423 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 3
diff changeset
424 maximise the value of each read
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
425
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
426 If ILLUMINACLIP is requested then it is always performed first; subsequent options
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
427 can be mixed and matched and will be performed in the order that they have been
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
428 specified.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
429
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
430 .. class:: warningmark
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
431
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
432 Note that trimming operation order is important.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
433
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
434 -------------
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
435
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
436 .. class:: infomark
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
437
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
438 **Inputs**
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
439
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
440 For single-end data this Trimmomatic tool accepts a single FASTQ file; for
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
441 paired-end data it will accept either two FASTQ files (R1 and R2), or a
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
442 dataset collection containing the R1/R2 FASTQ pair.
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
443
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
444 .. class:: infomark
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
445
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
446 **Outputs**
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
447
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
448 For paired-end data a particular strength of Trimmomatic is that it retains the
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
449 pairing of reads (from R1 and R2) in the filtered output files:
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
450
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
451 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
452 both have survived filtering.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
453 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
454 one of the pair failed the filtering steps.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
455
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
456 .. class:: warningmark
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
457
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
458 If the input consists of a dataset collection with the R1/R2 FASTQ pair then
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
459 the outputs will also inclue two dataset collections: one for the 'paired'
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
460 outputs and one for the 'unpaired' (as described above)
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
461
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
462 Retaining the same order and number of reads in the filtered output fastq files is
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
463 essential for many downstream analysis tools.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
464
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
465 For single-end data the output is a single FASTQ file containing just the filtered
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
466 reads.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
467
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
468 -------------
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
469
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
470 .. class:: infomark
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
471
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
472 **Credits**
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
473
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
474 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
8
415a165d92bb Uploaded v0.36.4.
pjbriggs
parents: 7
diff changeset
475 University of Manchester, with contributions from Peter van Heusden, Marius
11
59054f086eca Version 0.36.6 (output logs and handle fastqillumina and fastqsolexa inputs)
pjbriggs
parents: 10
diff changeset
476 van den Beek, Jelle Scholtalbers, Charles Girardot, and Matthias Bernt.
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
477
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
478 It runs the Trimmomatic program which has been developed
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
479 within Bjorn Usadel's group at RWTH Aachen university.
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
480
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
481 Trimmomatic website (including documentation):
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
482
6
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
pjbriggs
parents: 5
diff changeset
483 * http://www.usadellab.org/cms/index.php?page=trimmomatic
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
484
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
485 The reference for Trimmomatic is:
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
486
1
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
487 * Bolger, A.M., Lohse, M., &amp; Usadel, B. (2014). Trimmomatic: A flexible trimmer
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
488 for Illumina Sequence Data. Bioinformatics, btu170.
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
489
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
490 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
491 use it.
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents: 2
diff changeset
492 ]]></help>
1
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
493 <citations>
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
494 <!--
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
495 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
496 Can be either DOI or Bibtex
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
497 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
498 -->
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
499 <citation type="doi">10.1093/bioinformatics/btu170</citation>
2bd7cdbb6228 Add README and citation tags.
pjbriggs
parents: 0
diff changeset
500 </citations>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
501 </tool>