comparison trim_galore_wrapper.xml @ 2:9109c2c3be1e draft

Uploaded

1:898db63d2e84

    <!-- Wrapper compatible with Trim Galore version 0.2.8 -->
    <description>adaptive quality and adapter trimmer</description>
    <version_command interpreter="perl">trim_galore --version</version_command>
    <requirements>
        <requirement type="package" version="1.1">cutadapt</requirement>
        <requirement type="package" version="0.10.1">fastqc</requirement>
    </requirements>
    <command interpreter="perl">
        #from glob import glob
        #import tempfile, os

        ##


        #if $params.settingsType == "custom":

            $params.fastqc
            ## default 20
            --quality $params.quality
            ## default 'AGATCGGAAGAGC'
            #if $params.adapter.strip() != '':
                --adapter $params.adapter

            #end if
        #end if

        ## delete the temp_dir
        ##rm -rf $temp_dir

    </command>
    <inputs>

        <!-- Input Parameters -->

              <option value="custom">Full parameter list</option>
            </param>
            <when value="default" />
            <!-- Full/advanced params. -->
            <when value="custom">
                <param name="fastqc" type="boolean" truevalue="--fastqc" falsevalue="" checked="False" label="Run FastQC in the default mode on the FastQ file once trimming is complete" help="" />
                <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="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed">
                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
                </param>
                <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />

    <help>

**What it does**

TrimGalore!_ is a wrapper script that makes use of the publically available 
adapter trimming tool Cutadapt and FastQC for optional quality control once 
the trimming process has completed.


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

2:9109c2c3be1e

    <!-- Wrapper compatible with Trim Galore version 0.2.8 -->
    <description>adaptive quality and adapter trimmer</description>
    <version_command interpreter="perl">trim_galore --version</version_command>
    <requirements>
        <requirement type="package" version="1.1">cutadapt</requirement>
    </requirements>
    <command interpreter="perl">
        #from glob import glob
        #import tempfile, os

        ##


        #if $params.settingsType == "custom":

            ## default 20
            --quality $params.quality
            ## default 'AGATCGGAAGAGC'
            #if $params.adapter.strip() != '':
                --adapter $params.adapter

            #end if
        #end if

        ## delete the temp_dir
        rm -rf $temp_dir

    </command>
    <inputs>

        <!-- Input Parameters -->

              <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="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed">
                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
                </param>
                <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />

    <help>

**What it does**

TrimGalore!_ is a wrapper script that makes use of the publically available 
adapter trimming tool Cutadapt.


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