Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.xml @ 3:f8a9a5eaca8a draft
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
author | pjbriggs |
---|---|
date | Wed, 23 Sep 2015 08:59:23 -0400 |
parents | a60283899c6d |
children | 14d05f2d511d |
rev | line source |
---|---|
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.3"> |
0 | 2 <description>flexible read trimming tool for Illumina NGS data</description> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
3 <requirements> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
4 <requirement type="package" version="0.32">trimmomatic</requirement> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
5 </requirements> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
6 <stdio> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
7 <exit_code range="1:" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
8 </stdio> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
9 <command interpreter="bash"><![CDATA[ |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
10 trimmomatic.sh |
0 | 11 -mx8G |
12 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar | |
13 #if $paired_end.is_paired_end | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
14 PE -threads \${GALAXY_SLOTS:-6} -phred33 |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
15 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
16 #if $paired_input_type == "pair_of_files" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
17 "${paired_end.paired_input_type_conditional.fastq_r1_in}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
18 "${paired_end.paired_input_type_conditional.fastq_r2_in}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
19 "${fastq_out_r1_paired}" "${fastq_out_r1_unpaired}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
20 "${fastq_out_r2_paired}" "${fastq_out_r2_unpaired}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
21 #else |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
22 "${paired_end.paired_input_type_conditional.fastq_pair.forward}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
23 "${paired_end.paired_input_type_conditional.fastq_pair.reverse}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
24 "${fastq_out_paired.forward}" "${fastq_out_unpaired.forward}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
25 "${fastq_out_paired.reverse}" "${fastq_out_unpaired.reverse}" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
26 #end if |
0 | 27 #else |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
28 SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out" |
0 | 29 #end if |
30 ## ILLUMINACLIP option | |
31 #if $illuminaclip.do_illuminaclip | |
32 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold | |
33 #end if | |
34 ## Other operations | |
35 #for $op in $operations | |
36 ## SLIDINGWINDOW | |
37 #if str( $op.operation.name ) == "SLIDINGWINDOW" | |
38 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality | |
39 #end if | |
40 ## MINLEN:36 | |
41 #if str( $op.operation.name ) == "MINLEN" | |
42 MINLEN:$op.operation.minlen | |
43 #end if | |
44 #if str( $op.operation.name ) == "LEADING" | |
45 LEADING:$op.operation.leading | |
46 #end if | |
47 #if str( $op.operation.name ) == "TRAILING" | |
48 TRAILING:$op.operation.trailing | |
49 #end if | |
50 #if str( $op.operation.name ) == "CROP" | |
51 CROP:$op.operation.crop | |
52 #end if | |
53 #if str( $op.operation.name ) == "HEADCROP" | |
54 HEADCROP:$op.operation.headcrop | |
55 #end if | |
56 #end for | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
57 ]]></command> |
0 | 58 <inputs> |
59 <conditional name="paired_end"> | |
60 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> | |
61 <when value="no"> | |
62 <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" /> | |
63 </when> | |
64 <when value="yes"> | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
65 <conditional name="paired_input_type_conditional"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
66 <param name="paired_input_type" type="select" label="Input Type"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
67 <option value="pair_of_files" selected="true">Pair of datasets</option> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
68 <option value="collection">Dataset collection pair</option> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
69 </param> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
70 <when value="pair_of_files"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
71 <param name="fastq_r1_in" type="data" format="fastqsanger" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
72 label="Input FASTQ file (R1/first of pair)" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
73 <param name="fastq_r2_in" type="data" format="fastqsanger" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
74 label="Input FASTQ file (R2/second of pair)" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
75 </when> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
76 <when value="collection"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
77 <param name="fastq_pair" format="fastqsanger" type="data_collection" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
78 collection_type="paired" |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
79 label="Select FASTQ dataset collection with R1/R2 pair" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
80 </when> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
81 </conditional> |
0 | 82 </when> |
83 </conditional> | |
84 <conditional name="illuminaclip"> | |
85 <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="off" /> | |
86 <when value="yes"> | |
87 <param name="adapter_fasta" type="select" label="Adapter sequences to use"> | |
88 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> | |
89 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> | |
90 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> | |
91 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> | |
92 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> | |
93 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> | |
94 </param> | |
95 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> | |
96 <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" /> | |
97 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" /> | |
98 </when> | |
99 </conditional> | |
100 <repeat name="operations" title="Trimmomatic Operation" min="1"> | |
101 <conditional name="operation"> | |
102 <param name="name" type="select" label="Select Trimmomatic operation to perform"> | |
103 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> | |
104 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> | |
105 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> | |
106 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> | |
107 <option value="CROP">Cut the read to a specified length (CROP)</option> | |
108 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> | |
109 </param> | |
110 <when value="SLIDINGWINDOW"> | |
111 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> | |
112 <param name="required_quality" type="integer" label="Average quality required" value="20" /> | |
113 </when> | |
114 <when value="MINLEN"> | |
115 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> | |
116 </when> | |
117 <when value="LEADING"> | |
118 <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" /> | |
119 </when> | |
120 <when value="TRAILING"> | |
121 <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" /> | |
122 </when> | |
123 <when value="CROP"> | |
124 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> | |
125 </when> | |
126 <when value="HEADCROP"> | |
127 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> | |
128 </when> | |
129 </conditional> | |
130 </repeat> | |
131 </inputs> | |
132 <outputs> | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
133 <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)"> |
0 | 134 <filter>paired_end['is_paired_end']</filter> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
135 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
0 | 136 </data> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
137 <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)"> |
0 | 138 <filter>paired_end['is_paired_end']</filter> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
139 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
0 | 140 </data> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
141 <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)"> |
0 | 142 <filter>paired_end['is_paired_end']</filter> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
143 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
0 | 144 </data> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
145 <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)"> |
0 | 146 <filter>paired_end['is_paired_end']</filter> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
147 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
0 | 148 </data> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
149 <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}"> |
0 | 150 <filter>not paired_end['is_paired_end']</filter> |
151 </data> | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
152 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
153 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
154 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
155 <filter>paired_end['is_paired_end']</filter> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
156 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
157 </collection> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
158 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
159 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
160 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
161 <filter>paired_end['is_paired_end']</filter> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
162 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
163 </collection> |
0 | 164 </outputs> |
165 <tests> | |
166 <test> | |
167 <!-- Single-end example --> | |
168 <param name="is_paired_end" value="no" /> | |
169 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
170 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
171 <!-- | |
172 **NB** outputs have to be specified in order that they appear in the | |
173 tool (which is the order they will be written to the history) - the | |
174 test framework seems to use the order and ignores the "name" attribute | |
175 --> | |
176 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> | |
177 </test> | |
178 <test> | |
179 <!-- Paired-end example --> | |
180 <param name="is_paired_end" value="yes" /> | |
181 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
182 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
183 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
184 <!-- | |
185 **NB** outputs have to be specified in order that they appear in the | |
186 tool (which is the order they will be written to the history) - the | |
187 test framework seems to use the order and ignores the "name" attribute | |
188 --> | |
189 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> | |
190 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
191 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
192 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
193 </test> | |
194 <test> | |
195 <!-- Single-end example (cropping) --> | |
196 <param name="is_paired_end" value="no" /> | |
197 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
198 <param name="operations_0|operation|name" value="CROP" /> | |
199 <param name="operations_0|operation|crop" value="10" /> | |
200 <!-- | |
201 **NB** outputs have to be specified in order that they appear in the | |
202 tool (which is the order they will be written to the history) - the | |
203 test framework seems to use the order and ignores the "name" attribute | |
204 --> | |
205 <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> | |
206 </test> | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
207 <test> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
208 <!-- Paired-end with dataset collection --> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
209 <param name="is_paired_end" value="yes" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
210 <param name="paired_input_type" value="collection" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
211 <param name="fastq_pair"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
212 <collection type="paired"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
213 <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
|
214 <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
|
215 </collection> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
216 </param> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
217 <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
|
218 <output_collection name="fastq_out_paired" type="paired"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
219 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
220 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
221 </output_collection> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
222 <output_collection name="fastq_out_unpaired" type="paired"> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
223 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
224 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
225 </output_collection> |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
226 </test> |
0 | 227 </tests> |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
228 <help><![CDATA[ |
0 | 229 .. class:: infomark |
230 | |
231 **What it does** | |
232 | |
233 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and | |
234 single ended data. | |
235 | |
236 This tool allows the following trimming steps to be performed: | |
237 | |
238 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read | |
239 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average | |
240 quality within the window falls below a threshold | |
241 * **MINLEN:** Drop the read if it is below a specified length | |
242 * **LEADING:** Cut bases off the start of a read, if below a threshold quality | |
243 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality | |
244 * **CROP:** Cut the read to a specified length | |
245 * **HEADCROP:** Cut the specified number of bases from the start of the read | |
246 | |
247 If ILLUMINACLIP is requested then it is always performed first; subsequent options | |
248 can be mixed and matched and will be performed in the order that they have been | |
249 specified. | |
250 | |
251 .. class:: warningmark | |
252 | |
253 Note that trimming operation order is important. | |
254 | |
255 ------------- | |
256 | |
257 .. class:: infomark | |
258 | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
259 **Inputs** |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
260 |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
261 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
|
262 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
|
263 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
|
264 |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
265 .. class:: infomark |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
266 |
0 | 267 **Outputs** |
268 | |
269 For paired-end data a particular strength of Trimmomatic is that it retains the | |
270 pairing of reads (from R1 and R2) in the filtered output files: | |
271 | |
272 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where | |
273 both have survived filtering. | |
274 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where | |
275 one of the pair failed the filtering steps. | |
276 | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
277 .. class:: warningmark |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
278 |
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
279 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
|
280 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
|
281 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
|
282 |
0 | 283 Retaining the same order and number of reads in the filtered output fastq files is |
284 essential for many downstream analysis tools. | |
285 | |
286 For single-end data the output is a single FASTQ file containing just the filtered | |
287 reads. | |
288 | |
289 ------------- | |
290 | |
291 .. class:: infomark | |
292 | |
293 **Credits** | |
294 | |
295 This Galaxy tool has been developed within the Bioinformatics Core Facility at the | |
296 University of Manchester. It runs the Trimmomatic program which has been developed | |
297 within Bjorn Usadel's group at RWTH Aachen university. | |
298 | |
299 Trimmomatic website (including documentation): | |
300 | |
301 * http://www.usadellab.org/cms/index.php?page=trimmomatic | |
302 | |
303 The reference for Trimmomatic is: | |
304 | |
1 | 305 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer |
306 for Illumina Sequence Data. Bioinformatics, btu170. | |
0 | 307 |
308 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you | |
309 use it. | |
3
f8a9a5eaca8a
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
parents:
2
diff
changeset
|
310 ]]></help> |
1 | 311 <citations> |
312 <!-- | |
313 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
314 Can be either DOI or Bibtex | |
315 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
316 --> | |
317 <citation type="doi">10.1093/bioinformatics/btu170</citation> | |
318 </citations> | |
0 | 319 </tool> |