annotate tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 9:422724644e24 draft

"Update all the pico_galaxy tools on main Tool Shed"

<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4">
    <description>using the read name suffixes</description>
    <requirements>
        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
        <requirement type="package" version="1.67">biopython</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/fastq_paired_unpaired.py --version
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/fastq_paired_unpaired.py '$input_fastq.extension' '$input_fastq'
#if $output_choice_cond.output_choice=="separate"
 '$output_forward' '$output_reverse'
#elif $output_choice_cond.output_choice=="interleaved"
 '$output_paired'
#end if
$output_singles
    </command>
    <inputs>
        <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
        <conditional name="output_choice_cond">
            <param name="output_choice" type="select" label="How to output paired reads?">
                <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
                <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option>
            </param>
            <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
            <when value="separate" />
            <when value="interleaved" />
        </conditional>
    </inputs>
    <outputs>
        <data name="output_singles" format_source="input_fastq" label="Orphan or single reads"/>
        <data name="output_forward" format_source="input_fastq" label="Forward paired reads">
            <filter>output_choice_cond["output_choice"] == "separate"</filter>
        </data>
        <data name="output_reverse" format_source="input_fastq" label="Reverse paired reads">
            <filter>output_choice_cond["output_choice"] == "separate"</filter>
        </data>
        <data name="output_paired" format_source="input_fastq" label="Interleaved paired reads">
            <filter>output_choice_cond["output_choice"] == "interleaved"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
            <param name="output_choice" value="separate"/>
            <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
            <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/>
            <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/>
        </test>
        <test>
            <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
            <param name="output_choice" value="interleaved"/>
            <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
            <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/>
        </test>
    </tests>
    <help>

**What it does**

Using the common read name suffix conventions, it divides a FASTQ file into
paired reads, and orphan or single reads.

The input file should be a valid FASTQ file which has been sorted so that
any partner forward+reverse reads are consecutive. The output files all
preserve this sort order. Pairing are recognised based on standard name
suffixes. See below or run the tool with no arguments for more details.

Any reads where the forward/reverse naming suffix used is not recognised
are treated as orphan reads. The tool supports the /1 and /2 convention
originally used by Illumina, .f and .r convention, the Sanger convention
(see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details),
and the current Illumina convention where the reads get the same identifier
with the fragment number in the description, for example:

 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA

Note that this does support multiple forward and reverse reads per template
(which is quite common with Sanger sequencing), e.g. this which is sorted
alphabetically:

 * WTSI_1055_4p17.p1kapIBF
 * WTSI_1055_4p17.p1kpIBF
 * WTSI_1055_4p17.q1kapIBR
 * WTSI_1055_4p17.q1kpIBR

or this where the reads already come in pairs:

 * WTSI_1055_4p17.p1kapIBF
 * WTSI_1055_4p17.q1kapIBR
 * WTSI_1055_4p17.p1kpIBF
 * WTSI_1055_4p17.q1kpIBR

both become:

 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following paper:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
https://doi.org/10.7717/peerj.167

This tool is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
    </help>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
    </citations>
</tool>