comparison trim_galore.xml @ 9:1bfc7254232e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923

8:f1e71aeaa923

<tool id="trim_galore" name="Trim Galore!" version="0.4.2">
    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
    <description>adaptive quality and adapter trimmer</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">
                <param name="trimming_select" type="select" label="Trimming reads?">
                    <option value="">Automatic detection</option>
                    <option value="--illumina">Illumina universal</option>
                    <option value="--nextera">Nextera transposase</option>
                    <option value="--small_rna">Illumina small RNA adapters</option>
                    <option value="user">User defined adapter trimming</option>
                </param>
                <when value=""/>
                <when value="--illumina"/>
                <when value="--nextera"/>
                <when value="--small_rna"/>

            <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
                <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
                    This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
                    (--three_prime_clip_R1)</help>
            </param>
            <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
                <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
                    adapter/quality trimming has been performed. This may remove some unwanted bias from
                    the 3' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>
            </param>
        </macro>
    </macros>
    <requirements>
        <!-- conda dependency -->

              <option value="custom">Full parameter list</option>
            </param>
            <when value="default" />
            <!-- Full/advanced params. -->
            <when value="custom">
                <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal"
                    help="For more information please see below." />
                <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
                <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
                <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" />

                <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 1" />
                <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 2" />

                <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />

                <conditional name="retain_unpaired">
                    <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">

            <!-- Full/advanced params. -->
            <when value="custom">
                <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
                    label="Specifies that the input file was an MspI digested RRBS sample" />
                <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
                    label="Selecting this option for non-directional RRBS libraries" />
            </when>  <!-- full -->
        </conditional>  <!-- params -->

    </inputs>
    <outputs>

 * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1

.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

It is developed by Felix Krueger at the Babraham Institute.
]]>
    </help>
    <citations></citations>
</tool>

9:1bfc7254232e

<tool id="trim_galore" name="Trim Galore!" version="0.4.2">
    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
    <description>Quality and adapter trimmer of reads</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">
                <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
                    <option value="">Automatic detection</option>
                    <option value="--illumina">Illumina universal</option>
                    <option value="--nextera">Nextera transposase</option>
                    <option value="--small_rna">Illumina small RNA adapters</option>
                    <option value="user">User defined adapter sequence</option>
                </param>
                <when value=""/>
                <when value="--illumina"/>
                <when value="--nextera"/>
                <when value="--small_rna"/>

            <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
                <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
                    This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
                    (--three_prime_clip_R1)</help>
            </param>
            <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
                <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
                    adapter/quality trimming has been performed. This may remove some unwanted bias from
                    the 3' end that is not directly related to adapter sequence or basecall quality.</help>
            </param>
        </macro>
    </macros>
    <requirements>
        <!-- conda dependency -->

              <option value="custom">Full parameter list</option>
            </param>
            <when value="default" />
            <!-- Full/advanced params. -->
            <when value="custom">
                <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal (Enter phred quality score threshold)"
                    help="For more information please see below." />
                <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
                <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
                <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" />

                <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5' end of read 1" />
                <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5' end of read 2 (Only for paired-end reads)" />

                <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />

                <conditional name="retain_unpaired">
                    <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">

            <!-- Full/advanced params. -->
            <when value="custom">
                <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
                    label="Specifies that the input file was an MspI digested RRBS sample" />
                <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
                    label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
            </when>  <!-- full -->
        </conditional>  <!-- params -->

    </inputs>
    <outputs>

 * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1

.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

It is developed by Felix Krueger at the Babraham Institute.

----

**Main Settings**

* **Adapter sequence to be trimmed**

  * **Automatic detection**
    
      | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used.

  * **Illumina universal**

      | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.
      |
      | *option --illumina*

  * **Nextera transposase**

      | Adapter sequence to be trimmed is the first 12bp of the Nextera adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.
      |
      | *option --nextera*

  * **Illumina small RNA adapters**

      | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5' adapter automatically (‘GATCGTCGGACT’) unless -a 2 had been defined explicitly.
      |
      | *option --small_rna*

  * **User defined adapter trimming**

      | Adapter sequence to be trimmed is the sequence entered by the user instead of the default auto-detection of adapter sequence.
      |
      | *option -a*

* **If Single-End Reads**

  * **Remove <int> bp from the 3' end**

      | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
      |
      | *option --three_prime_clip_R1*

* **If Paired-End Reads**

  * **Trims 1 bp off every read from its 3' end**

      | This may be needed for FastQ files that are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards alignments like this:
      |
      |   R1 --------------------------->
      |   R2 <---------------------------
      |
      | or this:
      | 
      |   R1 ----------------------->
      |   R2 <-----------------
      |
      | as invalid (whenever a start/end coordinate is contained within the other read).
      |
      | *option --t*

  * **Remove <int> bp from the 3' end of read 1**

      | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
      |
      | *option --three_prime_clip_R1*

  * **Remove <int> bp from the 3' end of read 2**

      | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
      |
      | *option --three_prime_clip_R2*

----

**Advanced Settings**

* **Trim low-quality ends from reads in addition to adapter removal**

    | For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract <INT> from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Default Phred score: 20.
    |
    | *option -q*

* **Overlap with adapter sequence required to trim a sequence**

    | Defaults to a very stringent setting of '1', i.e. even a single bp of overlapping sequence will be trimmed of the 3' end of any read.
    |
    | *option -s*

* **Maximum allowed error rate**

    | (no. of errors divided by the length of the matching region) (default: 0.1).
    |
    | *option -e*

* **Discard reads that became shorter than length <INT>**

    | because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp.
    |
    | For paired-end files, both reads of a read-pair need to be longer than <INT> bp to be printed out to validated paired-end files (see option --paired). If only one read became too short there is the possibility of keeping such unpaired single-end reads (see --retain_unpaired). Default pair-cutoff: 20 bp.
    |
    | *option --length*

* **Instructs Trim Galore! to remove INT bp from the 5' end of read 1**

    | Instructs Trim Galore to remove <INT> bp from the 5' end of read 1 (or single-end reads). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. Default: OFF.
    |
    | *option --clip_R1*

* **Instructs Trim Galore! to remove INT bp from the 5' end of read 2**

    | Instructs Trim Galore to remove <int> bp from the 5' end of read 2 (paired-end reads only). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. For paired-end BS-Seq, it is recommended to remove the first few bp because the end-repair reaction may introduce a bias towards low methylation. Please refer to the M-bias plot section in the Bismark User Guide for some examples. Default: OFF.
    |
    | *option --clip_R2*

* **Specify if you would like to retain unpaired reads**

    | If only one of the two paired-end reads became too short, the longer read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output files. The length cutoff for unpaired single-end reads is governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF.
    |
    | *option --retained_unpaired*

----

**RRBS specific settings**

* **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)**

    | Sequences which were adapter-trimmed will have a further 2 bp removed from their 3' end. This is to avoid that the filled-in C close to the second MspI site in a sequence is used for methylation calls. Sequences which were merely trimmed because of poor quality will not be shortened further.
    |
    | *option -rrbs*

* **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**

    | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
    |
    | *option --non_directional*]]>
    </help>
    <citations></citations>
</tool>