trimmomatic: trimmomatic.xml annotate

annotate trimmomatic.xml @ 7:6eeacf19a38e draft

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).

author	pjbriggs
date	Tue, 21 Mar 2017 08:42:05 -0400
parents	141bba0e9a77
children	415a165d92bb

rev	line source
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	1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.3">
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>
4 14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	7 <requirement type="package" version="0.36">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 $readtype.single_or_paired in ["pair_of_files","collection"]
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	27 PE -threads \${GALAXY_SLOTS:-6} -phred33
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	28 fastq_r1.'$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.'$r2_ext'
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	31 #else
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	32 SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$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 $illuminaclip.do_illuminaclip
5 f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now). pjbriggs parents: 4 diff changeset	36 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	37 #end if
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	38 ## Other operations
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	39 #for $op in $operations
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	40 ## SLIDINGWINDOW
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	41 #if str( $op.operation.name ) == "SLIDINGWINDOW"
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	42 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	43 #end if
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	44 ## MINLEN:36
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	45 #if str( $op.operation.name ) == "MINLEN"
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	46 MINLEN:$op.operation.minlen
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	47 #end if
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	48 #if str( $op.operation.name ) == "LEADING"
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	49 LEADING:$op.operation.leading
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	50 #end if
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	51 #if str( $op.operation.name ) == "TRAILING"
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	52 TRAILING:$op.operation.trailing
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	53 #end if
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	54 #if str( $op.operation.name ) == "CROP"
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	55 CROP:$op.operation.crop
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	56 #end if
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	57 #if str( $op.operation.name ) == "HEADCROP"
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	58 HEADCROP:$op.operation.headcrop
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	59 #end if
4 14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	60 #if str( $op.operation.name ) == "AVGQUAL"
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	61 AVGQUAL:$op.operation.avgqual
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	62 #end if
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	63 #if str( $op.operation.name ) == "MAXINFO"
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	64 MAXINFO:$op.operation.target_length:$op.operation.strictness
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	65 #end if
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	66 #end for
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	67 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	68 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	69 &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	70 #if $readtype.single_or_paired == "pair_of_files"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	71 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	72 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	73 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	74 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	75 #elif $readtype.single_or_paired == "collection"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	76 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	77 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	78 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	79 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	80 #else
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	81 mv fastq_out.'$fastq_in.extension' '${fastq_out}'
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	82 #end if
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	83 ]]></command>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	84 <inputs>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	85 <conditional name="readtype">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	86 <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	87 <option value="se" selected="true">Single-end</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	88 <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	89 <option value="collection">Paired-end (as collection)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	90 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	91 <when value="se">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	92 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	93 </when>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	94 <when value="pair_of_files">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	95 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	96 label="Input FASTQ file (R1/first of pair)" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	97 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqgsanger.gz"
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	98 label="Input FASTQ file (R2/second of pair)" />
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	99 </when>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	100 <when value="collection">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	101 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	102 </when>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	103 </conditional>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	104 <conditional name="illuminaclip">
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	105 <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	106 <when value="yes">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	107 <param name="adapter_fasta" type="select" label="Adapter sequences to use">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	108 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	109 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	110 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	111 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	112 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	113 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	114 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	115 <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	116 <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	117 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	118 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	119 <when value="no" /> <!-- empty clause to satisfy planemo lint -->
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	120 </conditional>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	121 <repeat name="operations" title="Trimmomatic Operation" min="1">
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	122 <conditional name="operation">
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	123 <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	124 <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	125 <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	126 <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	127 <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	128 <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	129 <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	130 <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	131 <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	132 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	133 <when value="SLIDINGWINDOW">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	134 <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	135 <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	136 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	137 <when value="MINLEN">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	138 <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	139 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	140 <when value="LEADING">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	141 <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	142 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	143 <when value="TRAILING">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	144 <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	145 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	146 <when value="CROP">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	147 <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	148 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	149 <when value="HEADCROP">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	150 <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	151 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	152 <when value="AVGQUAL">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	153 <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	154 </when>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	155 <when value="MAXINFO">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	156 <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	157 <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 (<0.2) favours longer reads, high values (>0.8) favours read correctness." />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	158 </when>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	159 </conditional>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	160 </repeat>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	161 </inputs>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	162 <outputs>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	163 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	164 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	165 </data>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	166 <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	167 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	168 </data>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	169 <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	170 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	171 </data>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	172 <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	173 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	174 </data>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	175 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	176 <filter>readtype['single_or_paired'] == 'se'</filter>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	177 </data>
7 6eeacf19a38e Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek). pjbriggs parents: 6 diff changeset	178 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	179 <filter>readtype['single_or_paired'] == "collection"</filter>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	180 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	181 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	182 </collection>
7 6eeacf19a38e Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek). pjbriggs parents: 6 diff changeset	183 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	184 <filter>readtype['single_or_paired'] == "collection"</filter>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	185 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	186 <data name="reverse" label="${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	187 </collection>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	188
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	189 </outputs>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	190 <tests>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	191 <test>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	192 <!-- Single-end example -->
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	193 <param name="single_or_paired" value="se" />
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	194 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	195 <param name="operations_0\|operation\|name" value="SLIDINGWINDOW" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	196 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	197 </test>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	198 <test>
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	199 <!-- Single-end example - gzipped -->
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	200 <param name="single_or_paired" value="se" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	201 <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	202 <param name="operations_0\|operation\|name" value="SLIDINGWINDOW" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	203 <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	204 </test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	205 <test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	206 <!-- Paired-end example - gzipped -->
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	207 <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	208 <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	209 <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	210 <param name="operations_0\|operation\|name" value="SLIDINGWINDOW" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	211 <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	212 <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	213 <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	214 <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	215 </test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	216 <test>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	217 <!-- Paired-end example -->
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	218 <param name="single_or_paired" value="pair_of_files" />
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	219 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	220 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	221 <param name="operations_0\|operation\|name" value="SLIDINGWINDOW" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	222 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	223 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	224 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	225 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	226 </test>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	227 <test>
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	228 <!-- Single-end example (cropping) -->
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	229 <param name="single_or_paired" value="se" />
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	230 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	231 <param name="operations_0\|operation\|name" value="CROP" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	232 <param name="operations_0\|operation\|crop" value="10" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	233 <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	234 </test>
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	235 <test>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	236 <!-- Paired-end with dataset collection -->
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	237 <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	238 <param name="fastq_pair">
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	239 <collection type="paired">
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	240 <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	241 <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	242 </collection>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	243 </param>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	244 <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	245 <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	246 <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	247 <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	248 </output_collection>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	249 <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	250 <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	251 <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	252 </output_collection>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	253 </test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	254 <test>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	255 <!-- Paired-end with dataset collection - gzipped -->
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	256 <param name="single_or_paired" value="collection" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	257 <param name="fastq_pair">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	258 <collection type="paired">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	259 <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	260 <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	261 </collection>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	262 </param>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	263 <param name="operations_0\|operation\|name" value="SLIDINGWINDOW" />
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	264 <output_collection name="fastq_out_paired" type="paired">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	265 <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	266 <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	267 </output_collection>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	268 <output_collection name="fastq_out_unpaired" type="paired">
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	269 <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	270 <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	271 </output_collection>
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	272 </test>
4 14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	273 <test>
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	274 <!-- Single-end using AVGQUAL -->
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	275 <param name="single_or_paired" value="se" />
4 14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	276 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	277 <param name="operations_0\|operation\|name" value="AVGQUAL" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	278 <param name="operations_0\|operation\|avgqual" value="30" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	279 <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	280 </test>
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	281 <test>
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	282 <!-- Single-end using MAXINFO -->
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	283 <param name="single_or_paired" value="se" />
4 14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	284 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	285 <param name="operations_0\|operation\|name" value="MAXINFO" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	286 <param name="operations_0\|operation\|target_length" value="75" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	287 <param name="operations_0\|operation\|strictness" value="0.8" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	288 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	289 </test>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	290 </tests>
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	291 <help><![CDATA[
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	292 .. class:: infomark
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	293
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	294 What it does
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	295
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	296 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	297 single ended data.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	298
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	299 This tool allows the following trimming steps to be performed:
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	300
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	301 * ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	302 * SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	303 quality within the window falls below a threshold
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	304 * MINLEN: Drop the read if it is below a specified length
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	305 * LEADING: Cut bases off the start of a read, if below a threshold quality
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	306 * TRAILING: Cut bases off the end of a read, if below a threshold quality
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	307 * CROP: Cut the read to a specified length
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	308 * 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	309 * 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	310 * MAXINFO: Trim reads adaptively, balancing read length and error rate to
4 14d05f2d511d Version that supports Trimmomatic 0.36. pjbriggs parents: 3 diff changeset	311 maximise the value of each read
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	312
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	313 If ILLUMINACLIP is requested then it is always performed first; subsequent options
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	314 can be mixed and matched and will be performed in the order that they have been
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	315 specified.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	316
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	317 .. class:: warningmark
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	318
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	319 Note that trimming operation order is important.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	320
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	321 -------------
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	322
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	323 .. class:: infomark
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	324
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	325 Inputs
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	326
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	327 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	328 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	329 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	330
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	331 .. class:: infomark
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	332
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	333 Outputs
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	334
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	335 For paired-end data a particular strength of Trimmomatic is that it retains the
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	336 pairing of reads (from R1 and R2) in the filtered output files:
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	337
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	338 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	339 both have survived filtering.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	340 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	341 one of the pair failed the filtering steps.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	342
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	343 .. class:: warningmark
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	344
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	345 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	346 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	347 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	348
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	349 Retaining the same order and number of reads in the filtered output fastq files is
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	350 essential for many downstream analysis tools.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	351
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	352 For single-end data the output is a single FASTQ file containing just the filtered
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	353 reads.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	354
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	355 -------------
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	356
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	357 .. class:: infomark
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	358
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	359 Credits
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	360
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	361 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	362 University of Manchester, with contributions from Peter van Heusden and Marius
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	363 van den Beek.
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	364
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	365 It runs the Trimmomatic program which has been developed
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	366 within Bjorn Usadel's group at RWTH Aachen university.
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	367
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	368 Trimmomatic website (including documentation):
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	369
6 141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs) pjbriggs parents: 5 diff changeset	370 * http://www.usadellab.org/cms/index.php?page=trimmomatic
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	371
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	372 The reference for Trimmomatic is:
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	373
1 2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	374 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	375 for Illumina Sequence Data. Bioinformatics, btu170.
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	376
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	377 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	378 use it.
3 f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections) pjbriggs parents: 2 diff changeset	379 ]]></help>
1 2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	380 <citations>
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	381 <!--
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	382 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	383 Can be either DOI or Bibtex
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	384 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	385 -->
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	386 <citation type="doi">10.1093/bioinformatics/btu170</citation>
2bd7cdbb6228 Add README and citation tags. pjbriggs parents: 0 diff changeset	387 </citations>
0 3358c3d30143 Uploaded initial version. pjbriggs parents: diff changeset	388 </tool>

Mercurial > repos > pjbriggs > trimmomatic

annotate trimmomatic.xml @ 7:6eeacf19a38e draft