annotate ngs-tools_sample.xml @ 1:c72bbd681253 draft default tip

Updated to use ngs-tools 0.1.8.

<tool id="ngs-tools_sample" name="Sample (ngs-tools)" version="1.0.0">
	<description></description>
    <requirements>
        <requirement type="package" version="0.1.8">ngs-tools</requirement>
    </requirements>
    <command>
        ngs-tools sample
            --input-format $input_format.format
            --sample-size $size
            --output $output_file
            #if str($input_format.paired.paired_selector) == "True"
                --output-pair $output_file_pair
            #end if
            $input_format.paired.input_file
            #if str($input_format.paired.paired_selector) == "True"
                $input_format.paired.input_file_pair
            #end if
    </command>
    <inputs>
        <conditional name="input_format">
            <param name="format" type="select" label="Input format">
                <option value="fastq" selected="true">Fastq</option>
            </param>
            <when value="fastq">
                <conditional name="paired">
                    <param name="paired_selector" type="select" label="Paired data?">
                        <option value="True">Yes</option>
                        <option value="False" selected="true">No</option>
                    </param>
                    <when value="True">
                        <param name="input_file" type="data" format="fastq" label="FASTQ File to sample from" />
                        <param name="input_file_pair" type="data" format="fastq" label="FASTQ Paired File to sample from" />
                    </when>
                    <when value="False">
                        <param name="input_file" type="data" format="fastq" label="FASTQ File to sample from" />
                    </when>
                </conditional>
            </when>
        </conditional>
        <param name="size" type="integer" size="6" value="100" label="Number of records to sample" />
    </inputs>
    <outputs>
        <data name="output_file" format="input" />
        <data name="output_file_pair" format="input">
            <filter>input_format['paired']['paired_selector'] == "True"</filter>
        </data> 
    </outputs>
<help>

**What it does**

This tool samples a random number of records from the input file(s). Supports
paired data assuming paired files are in sync.

Supported formats: FASTQ.

--------

This tool is based on `ngs-tools`__ by Carlos Borroto &lt;[e-mail]&gt;.

 .. __: https://github.com/cjav/ngs-tools/
 
</help>
</tool>