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comparison trimmomatic.xml @ 4:2801d3cd21ee draft

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Updated to Trimmomatic 0.36.
author pjbriggs
date Thu, 14 Jul 2016 09:06:00 -0400
parents a7139c612c45
children b0315888eb4d
comparison
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3:a7139c612c45 4:2801d3cd21ee
1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.3"> 1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.0">
2 <description>flexible read trimming tool for Illumina NGS data</description> 2 <description>flexible read trimming tool for Illumina NGS data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.32">trimmomatic</requirement> 4 <requirement type="package" version="0.36">trimmomatic</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command interpreter="bash"><![CDATA[ 9 <command interpreter="bash"><![CDATA[
10 trimmomatic.sh 10 trimmomatic.sh
11 -mx8G 11 -mx8G
12 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar 12 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.36.jar
13 #if $paired_end.is_paired_end 13 #if $paired_end.is_paired_end
14 PE -threads \${GALAXY_SLOTS:-6} -phred33 14 PE -threads \${GALAXY_SLOTS:-6} -phred33
15 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type 15 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
16 #if $paired_input_type == "pair_of_files" 16 #if $paired_input_type == "pair_of_files"
17 "${paired_end.paired_input_type_conditional.fastq_r1_in}" 17 "${paired_end.paired_input_type_conditional.fastq_r1_in}"
50 #if str( $op.operation.name ) == "CROP" 50 #if str( $op.operation.name ) == "CROP"
51 CROP:$op.operation.crop 51 CROP:$op.operation.crop
52 #end if 52 #end if
53 #if str( $op.operation.name ) == "HEADCROP" 53 #if str( $op.operation.name ) == "HEADCROP"
54 HEADCROP:$op.operation.headcrop 54 HEADCROP:$op.operation.headcrop
55 #end if
56 #if str( $op.operation.name ) == "AVGQUAL"
57 AVGQUAL:$op.operation.avgqual
58 #end if
59 #if str( $op.operation.name ) == "MAXINFO"
60 MAXINFO:$op.operation.target_length:$op.operation.strictness
55 #end if 61 #end if
56 #end for 62 #end for
57 ]]></command> 63 ]]></command>
58 <inputs> 64 <inputs>
59 <conditional name="paired_end"> 65 <conditional name="paired_end">
94 </param> 100 </param>
95 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> 101 <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" /> 102 <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" /> 103 <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> 104 </when>
105 <when value="no" /> <!-- empty clause to satisfy planemo lint -->
99 </conditional> 106 </conditional>
100 <repeat name="operations" title="Trimmomatic Operation" min="1"> 107 <repeat name="operations" title="Trimmomatic Operation" min="1">
101 <conditional name="operation"> 108 <conditional name="operation">
102 <param name="name" type="select" label="Select Trimmomatic operation to perform"> 109 <param name="name" type="select" label="Select Trimmomatic operation to perform">
103 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> 110 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
104 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> 111 <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> 112 <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> 113 <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> 114 <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> 115 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
116 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
117 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
109 </param> 118 </param>
110 <when value="SLIDINGWINDOW"> 119 <when value="SLIDINGWINDOW">
111 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> 120 <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" /> 121 <param name="required_quality" type="integer" label="Average quality required" value="20" />
113 </when> 122 </when>
123 <when value="CROP"> 132 <when value="CROP">
124 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> 133 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
125 </when> 134 </when>
126 <when value="HEADCROP"> 135 <when value="HEADCROP">
127 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> 136 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
137 </when>
138 <when value="AVGQUAL">
139 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
140 </when>
141 <when value="MAXINFO">
142 <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." />
143 <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." />
128 </when> 144 </when>
129 </conditional> 145 </conditional>
130 </repeat> 146 </repeat>
131 </inputs> 147 </inputs>
132 <outputs> 148 <outputs>
222 <output_collection name="fastq_out_unpaired" type="paired"> 238 <output_collection name="fastq_out_unpaired" type="paired">
223 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> 239 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
224 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> 240 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
225 </output_collection> 241 </output_collection>
226 </test> 242 </test>
243 <test>
244 <!-- Single-end using AVGQUAL -->
245 <param name="is_paired_end" value="no" />
246 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
247 <param name="operations_0|operation|name" value="AVGQUAL" />
248 <param name="operations_0|operation|avgqual" value="30" />
249 <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
250 </test>
251 <test>
252 <!-- Single-end using MAXINFO -->
253 <param name="is_paired_end" value="no" />
254 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
255 <param name="operations_0|operation|name" value="MAXINFO" />
256 <param name="operations_0|operation|target_length" value="75" />
257 <param name="operations_0|operation|strictness" value="0.8" />
258 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
259 </test>
227 </tests> 260 </tests>
228 <help><![CDATA[ 261 <help><![CDATA[
229 .. class:: infomark 262 .. class:: infomark
230 263
231 **What it does** 264 **What it does**
241 * **MINLEN:** Drop the read if it is below a specified length 274 * **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 275 * **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 276 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
244 * **CROP:** Cut the read to a specified length 277 * **CROP:** Cut the read to a specified length
245 * **HEADCROP:** Cut the specified number of bases from the start of the read 278 * **HEADCROP:** Cut the specified number of bases from the start of the read
279 * **AVGQUAL:** Drop the read if the average quality is below a specified value
280 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to
281 maximise the value of each read
246 282
247 If ILLUMINACLIP is requested then it is always performed first; subsequent options 283 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 284 can be mixed and matched and will be performed in the order that they have been
249 specified. 285 specified.
250 286