view velvet/velveth_jgi.xml @ 0:4afe13ac23b6 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

<tool id="velveth_jgi" name="velveth" version="1.0.0">
<description>Preprocess sequences for velvet assembly</description>
<command interpreter='perl'>velveth_jgi_wrapper.pl $output $output.extra_files_path
velveth $output.extra_files_path $hash_length $strand_specific
#for $i in $short.files
$short.libtype $i.filetype.select $i.filetype.file
#end for
#for $i in $short2.files
$short2.libtype $i.filetype.select $i.filetype.file
#end for
#for $i in $short3.files
$short3.libtype $i.filetype.select $i.filetype.file
#end for
#for $i in $short4.files
$short4.libtype $i.filetype.select $i.filetype.file
#end for
#for $i in $short5.files
$short5.libtype $i.filetype.select $i.filetype.file
#end for
#for $i in $long.files
$long.libtype $i.filetype.select $i.filetype.file
#end for
</command>
<inputs>
    <param name="hash_length" type="integer" value='21' label="Hash length. Odd numbers only. Maximum 75."/>
    <param name="strand_specific" type='boolean' label="All libraries strand-specific?" truevalue='-strand_specific' falsevalue=''/>

    <conditional name="short">
        <param name="libtype" type="select" label="Short Library Type">
            <option value="-shortPaired">Paired</option>
            <option value="-short">Unpaired</option>
        </param>
        <when value="-shortPaired">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value="-short">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
    </conditional>

    <conditional name="short2">
        <param name="libtype" type="select" label="Short2 Library Type">
            <option value="-shortPaired2">Paired</option>
            <option value="-short2">Unpaired</option>
        </param>
        <when value="-shortPaired2">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value="-short2">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
    </conditional>

    <conditional name="short3">
        <param name="libtype" type="select" label="Short3 Library Type">
            <option value="-shortPaired3">Paired</option>
            <option value="-short3">Unpaired</option>
        </param>
        <when value="-shortPaired3">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value="-short3">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
    </conditional>

    <conditional name="short4">
        <param name="libtype" type="select" label="Short4 Library Type">
            <option value="-shortPaired4">Paired</option>
            <option value="-short4">Unpaired</option>
        </param>
        <when value="-shortPaired4">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value="-short4">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
    </conditional>

    <conditional name="short5">
        <param name="libtype" type="select" label="Short5 Library Type">
            <option value="-shortPaired5">Paired</option>
            <option value="-short5">Unpaired</option>
        </param>
        <when value="-shortPaired5">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value="-short5">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
    </conditional>

    <conditional name="long">
        <param name="libtype" type="select" label="Long Library Type">
            <option value="-longPaired">Paired</option>
            <option value="-long">Unpaired</option>
        </param>
        <when value="-longPaired">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value="-long">
            <repeat name="files" title="Files">
                <conditional name="filetype">
                    <param name='select' type='select' label='File Type'>
                        <option value='-fastq'>Fastq</option>
                        <option value='-fasta'>Fasta</option>
                    </param>
                    <when value="-fasta">
                        <param name="file" type="data" format="fasta" label="File"/>
                    </when>
                    <when value="-fastq">
                        <param name="file" type="data" format="fastq" label="File"/>
                    </when>
                </conditional>
            </repeat>
        </when>
    </conditional>
</inputs>
<outputs>
    <data name="output" format="velveth"/>
</outputs>

<help>

**What it does**

This tool preprocesses the sequence data using the specified hash length.  A larger hash length increases sensitivity at the expense of read depth.

**Manual**

http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
</help>
</tool>