comparison trimmomatic.xml @ 6:141bba0e9a77 draft

Uploaded v0.36.2 (adds support for compressed fastq inputs)

5:f80107cdc406

<tool id="trimmomatic" name="Trimmomatic" version="0.36.1">
  <description>flexible read trimming tool for Illumina NGS data</description>
  <macros>
    <import>trimmomatic_macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.36">trimmomatic</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
  @CONDA_TRIMMOMATIC_JAR_PATH@ &&
  @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
  java -mx8G -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
  #if $paired_end.is_paired_end
    PE -threads \${GALAXY_SLOTS:-6} -phred33
    #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
    #if $paired_input_type == "pair_of_files"
      "${paired_end.paired_input_type_conditional.fastq_r1_in}"
      "${paired_end.paired_input_type_conditional.fastq_r2_in}"
      "${fastq_out_r1_paired}" "${fastq_out_r1_unpaired}"
      "${fastq_out_r2_paired}" "${fastq_out_r2_unpaired}"
    #else
      "${paired_end.paired_input_type_conditional.fastq_pair.forward}"
      "${paired_end.paired_input_type_conditional.fastq_pair.reverse}"
      "${fastq_out_paired.forward}" "${fastq_out_unpaired.forward}"
      "${fastq_out_paired.reverse}" "${fastq_out_unpaired.reverse}"
    #end if
  #else
    SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out"
  #end if
  ## ILLUMINACLIP option
  #if $illuminaclip.do_illuminaclip
    ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
  #end if

      MAXINFO:$op.operation.target_length:$op.operation.strictness
    #end if
  #end for
  2>&1 | tee trimmomatic.log &&
  if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
  ]]></command>
  <inputs>
    <conditional name="paired_end">
    <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
    <when value="no">
      <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />
    </when>
    <when value="yes">
      <conditional name="paired_input_type_conditional">
        <param name="paired_input_type" type="select" label="Input Type">
          <option value="pair_of_files" selected="true">Pair of datasets</option>
          <option value="collection">Dataset collection pair</option>
        </param>
        <when value="pair_of_files">
 	  <param name="fastq_r1_in" type="data" format="fastqsanger"
		 label="Input FASTQ file (R1/first of pair)" />
 	  <param name="fastq_r2_in" type="data" format="fastqsanger"
		 label="Input FASTQ file (R2/second of pair)" />
	</when>
        <when value="collection">
          <param name="fastq_pair" format="fastqsanger" type="data_collection"
 		 collection_type="paired"
 		 label="Select FASTQ dataset collection with R1/R2 pair" />
        </when>
      </conditional>
    </when>
    </conditional>
    <conditional name="illuminaclip">
    <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" />
    <when value="yes">
      <param name="adapter_fasta" type="select" label="Adapter sequences to use">
	<option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
	<option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
	<option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
	<option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
	<option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
	<option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
      </param>
      <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
      <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" />
      <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
    </when>
    <when value="no" /> <!-- empty clause to satisfy planemo lint -->
    </conditional>
    <repeat name="operations" title="Trimmomatic Operation" min="1">
      <conditional name="operation">
	<param name="name" type="select" label="Select Trimmomatic operation to perform">
	  <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
	  <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
	  <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
	  <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
	  <option value="CROP">Cut the read to a specified length (CROP)</option>
	  <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
	  <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
	  <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
	</param>
	<when value="SLIDINGWINDOW">
	  <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
	  <param name="required_quality" type="integer" label="Average quality required" value="20" />
	</when>
	<when value="MINLEN">
	  <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
	</when>
	<when value="LEADING">
	  <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" />
	</when>
	<when value="TRAILING">
	  <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" />
	</when>
	<when value="CROP">
	  <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
	</when>
	<when value="HEADCROP">
	  <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
	</when>
	<when value="AVGQUAL">
	  <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
	</when>
	<when value="MAXINFO">
	  <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." />
	  <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." />
	</when>
      </conditional>
    </repeat>
  </inputs>
  <outputs>
    <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)">
      <filter>paired_end['is_paired_end']</filter>
      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
    </data>
    <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)">
      <filter>paired_end['is_paired_end']</filter>
      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
    </data>
    <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)">
      <filter>paired_end['is_paired_end']</filter>
      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
    </data>
    <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)">
      <filter>paired_end['is_paired_end']</filter>
      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
    </data>
    <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}">
      <filter>not paired_end['is_paired_end']</filter>
    </data>
    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired">
      <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" />
      <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" />
      <filter>paired_end['is_paired_end']</filter>
      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
    </collection>
    <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired">
      <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" />
      <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" />
      <filter>paired_end['is_paired_end']</filter>
      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
    </collection>
  </outputs>
  <tests>
    <test>
      <!-- Single-end example -->
      <param name="is_paired_end" value="no" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <!-- 
      **NB** outputs have to be specified in order that they appear in the
      tool (which is the order they will be written to the history) - the
      test framework seems to use the order and ignores the "name" attribute
      -->
      <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
    </test>
    <test>
      <!-- Paired-end example -->
      <param name="is_paired_end" value="yes" />
      <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <!-- 
      **NB** outputs have to be specified in order that they appear in the
      tool (which is the order they will be written to the history) - the
      test framework seems to use the order and ignores the "name" attribute
      -->
      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
    </test>
    <test>
      <!-- Single-end example (cropping) -->
      <param name="is_paired_end" value="no" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="CROP" />
      <param name="operations_0|operation|crop" value="10" />
      <!-- 
      **NB** outputs have to be specified in order that they appear in the
      tool (which is the order they will be written to the history) - the
      test framework seems to use the order and ignores the "name" attribute
      -->
      <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
    </test>
    <test>
      <!-- Paired-end with dataset collection -->
      <param name="is_paired_end" value="yes" />
      <param name="paired_input_type" value="collection" />
      <param name="fastq_pair">
        <collection type="paired">
          <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
          <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
        </collection>
      </param>
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output_collection name="fastq_out_paired" type="paired">
	<element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
	<element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
      </output_collection>
      <output_collection name="fastq_out_unpaired" type="paired">
	<element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
	<element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
      </output_collection>
    </test>
    <test>
      <!-- Single-end using AVGQUAL -->
      <param name="is_paired_end" value="no" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="AVGQUAL" />
      <param name="operations_0|operation|avgqual" value="30" />
      <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
    </test>
    <test>
      <!-- Single-end using MAXINFO -->
      <param name="is_paired_end" value="no" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="MAXINFO" />
      <param name="operations_0|operation|target_length" value="75" />
      <param name="operations_0|operation|strictness" value="0.8" />
      <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />

 * **LEADING:** Cut bases off the start of a read, if below a threshold quality
 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
 * **CROP:** Cut the read to a specified length
 * **HEADCROP:** Cut the specified number of bases from the start of the read
 * **AVGQUAL:** Drop the read if the average quality is below a specified value
 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to 
   maximise the value of each read

If ILLUMINACLIP is requested then it is always performed first; subsequent options
can be mixed and matched and will be performed in the order that they have been
specified.

.. class:: infomark

**Credits**

This Galaxy tool has been developed within the Bioinformatics Core Facility at the
University of Manchester. It runs the Trimmomatic program which has been developed
within Bjorn Usadel's group at RWTH Aachen university.

Trimmomatic website (including documentation):

 * http://www.usadellab.org/cms/index.php?page=trimmomatic 

The reference for Trimmomatic is:

 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
   for Illumina Sequence Data. Bioinformatics, btu170.

6:141bba0e9a77

<tool id="trimmomatic" name="Trimmomatic" version="0.36.2">
  <description>flexible read trimming tool for Illumina NGS data</description>
  <macros>
    <import>trimmomatic_macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.36">trimmomatic</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
  @CONDA_TRIMMOMATIC_JAR_PATH@ &&
  @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
  #if $readtype.single_or_paired == "pair_of_files"
    #set r1_ext = $readtype.fastq_r1_in.extension
    #set r2_ext = $readtype.fastq_r2_in.extension
    ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' &&
    ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' &&
  #elif $readtype.single_or_paired == "collection"
    #set r1_ext = $readtype.fastq_pair.forward.extension
    #set r2_ext = $readtype.fastq_pair.reverse.extension
    ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' &&
    ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' &&
  #else
    ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
  #end if
  java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
  #if $readtype.single_or_paired in ["pair_of_files","collection"]
    PE -threads \${GALAXY_SLOTS:-6} -phred33
      fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
      fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
      fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
  #else
    SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
  #end if
  ## ILLUMINACLIP option
  #if $illuminaclip.do_illuminaclip
    ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
  #end if

      MAXINFO:$op.operation.target_length:$op.operation.strictness
    #end if
  #end for
  2>&1 | tee trimmomatic.log &&
  if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
  &&
  #if $readtype.single_or_paired  == "pair_of_files"
    mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
    mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
    mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
    mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
  #elif $readtype.single_or_paired  == "collection"
    mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
    mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
    mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
    mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
  #else
    mv fastq_out.'$fastq_in.extension' '${fastq_out}'
  #end if
  ]]></command>
  <inputs>
    <conditional name="readtype">
      <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
         <option value="se" selected="true">Single-end</option>
         <option value="pair_of_files">Paired-end (two separate input files)</option>
         <option value="collection">Paired-end (as collection)</option>
      </param>
    <when value="se">
      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
    </when>
    <when value="pair_of_files">
      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz"
         label="Input FASTQ file (R1/first of pair)" />
      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqgsanger.gz"
         label="Input FASTQ file (R2/second of pair)" />
    </when>
      <when value="collection">
        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
      </when>
    </conditional>
    <conditional name="illuminaclip">
      <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" />
      <when value="yes">
        <param name="adapter_fasta" type="select" label="Adapter sequences to use">
          <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
          <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
          <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
          <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
          <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
          <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
        </param>
        <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
        <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" />
        <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
      </when>
      <when value="no" /> <!-- empty clause to satisfy planemo lint -->
    </conditional>
    <repeat name="operations" title="Trimmomatic Operation" min="1">
      <conditional name="operation">
        <param name="name" type="select" label="Select Trimmomatic operation to perform">
          <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
          <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
          <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
          <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
          <option value="CROP">Cut the read to a specified length (CROP)</option>
          <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
          <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
          <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
        </param>
        <when value="SLIDINGWINDOW">
          <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
          <param name="required_quality" type="integer" label="Average quality required" value="20" />
        </when>
        <when value="MINLEN">
          <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
        </when>
        <when value="LEADING">
          <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" />
        </when>
        <when value="TRAILING">
          <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" />
        </when>
        <when value="CROP">
          <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
        </when>
        <when value="HEADCROP">
          <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
        </when>
        <when value="AVGQUAL">
          <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
        </when>
        <when value="MAXINFO">
          <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." />
          <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." />
        </when>
      </conditional>
    </repeat>
  </inputs>
  <outputs>
    <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
      <filter>readtype['single_or_paired'] == 'se'</filter>
    </data>
    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired">
      <filter>readtype['single_or_paired'] == "collection"</filter>
      <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
      <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
    </collection>
      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired">
        <filter>readtype['single_or_paired'] == "collection"</filter>
        <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
        <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
    </collection>

  </outputs>
  <tests>
    <test>
      <!-- Single-end example -->
      <param name="single_or_paired" value="se" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
    </test>
    <test>
      <!-- Single-end example - gzipped -->
      <param name="single_or_paired" value="se" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" />
    </test>
    <test>
      <!-- Paired-end example - gzipped -->
      <param name="single_or_paired" value="pair_of_files" />
      <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
      <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
    </test>
    <test>
      <!-- Paired-end example -->
      <param name="single_or_paired" value="pair_of_files" />
      <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
    </test>
    <test>
      <!-- Single-end example (cropping) -->
      <param name="single_or_paired" value="se" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="CROP" />
      <param name="operations_0|operation|crop" value="10" />
      <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
    </test>
    <test>
      <!-- Paired-end with dataset collection -->
      <param name="single_or_paired" value="collection" />
      <param name="fastq_pair">
        <collection type="paired">
          <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
          <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
        </collection>
      </param>
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output_collection name="fastq_out_paired" type="paired">
        <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
        <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
      </output_collection>
      <output_collection name="fastq_out_unpaired" type="paired">
        <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
        <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
      </output_collection>
    </test>
    <test>
      <!-- Paired-end with dataset collection - gzipped -->
      <param name="single_or_paired" value="collection" />
      <param name="fastq_pair">
        <collection type="paired">
          <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
          <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/>
        </collection>
      </param>
      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
      <output_collection name="fastq_out_paired" type="paired">
        <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
        <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
      </output_collection>
      <output_collection name="fastq_out_unpaired" type="paired">
        <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
        <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
      </output_collection>
    </test>
    <test>
      <!-- Single-end using AVGQUAL -->
      <param name="single_or_paired" value="se" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="AVGQUAL" />
      <param name="operations_0|operation|avgqual" value="30" />
      <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
    </test>
    <test>
      <!-- Single-end using MAXINFO -->
      <param name="single_or_paired" value="se" />
      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
      <param name="operations_0|operation|name" value="MAXINFO" />
      <param name="operations_0|operation|target_length" value="75" />
      <param name="operations_0|operation|strictness" value="0.8" />
      <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />

 * **LEADING:** Cut bases off the start of a read, if below a threshold quality
 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
 * **CROP:** Cut the read to a specified length
 * **HEADCROP:** Cut the specified number of bases from the start of the read
 * **AVGQUAL:** Drop the read if the average quality is below a specified value
 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to
   maximise the value of each read

If ILLUMINACLIP is requested then it is always performed first; subsequent options
can be mixed and matched and will be performed in the order that they have been
specified.

.. class:: infomark

**Credits**

This Galaxy tool has been developed within the Bioinformatics Core Facility at the
University of Manchester, with contributions from Peter van Heusden and Marius
van den Beek.

It runs the Trimmomatic program which has been developed
within Bjorn Usadel's group at RWTH Aachen university.

Trimmomatic website (including documentation):

 * http://www.usadellab.org/cms/index.php?page=trimmomatic

The reference for Trimmomatic is:

 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
   for Illumina Sequence Data. Bioinformatics, btu170.