view tools/sample_seqs/sample_seqs.xml @ 0:3a807e5ea6c8 draft

Uploaded v0.0.1

<tool id="sample_seqs" name="Sub-sample sequences files" version="0.0.1">
    <description>e.g. to reduce coverage</description>
    <requirements>
        <requirement type="package" version="1.63">biopython</requirement>
        <requirement type="python-module">Bio</requirement>
    </requirements>
    <version_command interpreter="python">sample_seqs.py --version</version_command>
    <command interpreter="python">
#if str($sampling.type) == "everyNth":
sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" "${sampling.every_n}"
#elif str($sampling.type) == "percentage":
sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" "${sampling.percent}"
#else:
##Should give an error about invalid sampling type:
sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}"
#end if
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file" help="FASTA, FASTQ, or SFF format." />
        <conditional name="sampling">
            <param name="type" type="select" label="Sub-sampling approach">
                <option value="everyNth">Take every N-th sequence (e.g. every fifth sequence)</option>
                <option value="percentage">Take some percentage of the sequences (e.g. 20% will take every fifth sequence)</option>
                <!-- TODO - target coverage etc -->
            </param>
            <when value="everyNth">
                <param name="every_n" value="5" type="integer" min="2" label="N" help="At least 2, e.g. 5 will take every 5th sequence (taking 20% of the sequences)" />
            </when>
            <when value="percentage">
                <param name="percent" value="20.0" type="float" min="0" max="100" label="Percentage" help="Between 0 and 100, e.g. 20% will take every 5th sequence" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_file" format="input" metadata_source="input_file" label="${input_file.name} (sub-sampled)"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="get_orf_input.Suis_ORF.prot.fasta" />
            <param name="type" value="everyNth" />
            <param name="every_n" value="100" />
            <output name="output_file" file="get_orf_input.Suis_ORF.prot.sample_N100.fasta" />
        </test>
        <test>
            <param name="input_file" value="ecoli.fastq" />
            <param name="type" value="everyNth" />
            <param name="every_n" value="100" />
            <output name="output_file" file="ecoli.sample_N100.fastq" />
        </test>
        <test>
            <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
            <param name="type" value="everyNth" />
            <param name="every_n" value="5" />
            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff" ftype="sff"/>
        </test>
        <test>
            <param name="input_file" value="get_orf_input.Suis_ORF.prot.fasta" />
            <param name="type" value="percentage" />
            <param name="percent" value="1.0" />
            <output name="output_file" file="get_orf_input.Suis_ORF.prot.sample_N100.fasta" />
        </test>
        <test>
            <param name="input_file" value="ecoli.fastq" />
            <param name="type" value="percentage" />
            <param name="percent" value="1.0" />
            <output name="output_file" file="ecoli.sample_N100.fastq" />
        </test>
        <test>
            <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
            <param name="type" value="percentage" />
            <param name="percent" value="20.0" />
            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff" ftype="sff"/>
        </test>
    </tests>
    <help>
**What it does**

Takes an input file of sequences (typically FASTA or FASTQ, but also
Standard Flowgram Format (SFF) is supported), and returns a new sequence
file sub-sampling from this (in the same format).

Several sampling modes are supported, all designed to be non-random. This
allows reproducibility, and also works on paired sequence files. Also
note that by sampling uniformly through the file, this avoids any bias
should reads in any part of the file are of lesser quality (e.g. one part
of the slide).

The simplest mode is to take every N-th sequence, for example taking
every 2nd sequence would sample half the file - while taking every 5th
sequence would take 20% of the file.


**Example Usage**

Suppose you have some Illumina paired end data as files ``R1.fastq`` and
``R2.fastq`` which give an estimated x200 coverage, and you wish to do a
*de novo* assembly with a tool like MIRA which recommends lower coverage.
Taking every 3rd read would reduce the estimated coverage to about x66,
and would preserve the pairing as well.


**Citation**

This tool uses Biopython, so if you use this Galaxy tool in work leading to a
scientific publication please cite the following paper:

Cock et al (2009). Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This tool is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
    </help>
</tool>