annotate tools/seq_rename/seq_rename.xml @ 3:e1398f2ba9fe draft default tip

v0.0.8 galaxy_sequence_utils dependency etc

<tool id="seq_rename" name="Rename sequences" version="0.0.8">
    <description>with ID mapping from a tabular file</description>
    <requirements>
        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
        <requirement type="package" version="1.67">biopython</requirement>
        <requirement type="python-module">Bio</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">seq_rename.py --version</version_command>
    <command interpreter="python">
seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
    </command>
    <inputs>
        <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
        <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
        <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/>
        <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/>
    </inputs>
    <outputs>
        <data name="output_file" format_source="input_file" metadata_source="input_file" label="Renamed ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
            <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" />
            <param name="old_column" value="1" />
            <param name="new_column" value="2" />
            <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" />
        </test>
        <test>
            <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
            <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" />
            <param name="old_column" value="c1" />
            <param name="new_column" value="c2" />
            <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" />
        </test>
    </tests>
    <help>
**What it does**

Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
new sequence file (of the same format) where the sequence identifiers have been
renamed according to the specified columns in your tabular file.

Any original description is preserved (N/A for the SFF file format).

WARNING: If you have any duplicates in the input sequence file, you will still
have duplicate sequences in the output.

WARNING: If the tabular file has more than one new name for any old ID, the
last one is used.

WARNING: The old and new names in your tabular file should not contain white space.
If they do, only the first word is used as the identifier.

**References**

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

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
http://dx.doi.org/10.7717/peerj.167

This tool uses Biopython to read and write SFF files, so you may also wish to
cite the Biopython application note (and Galaxy too of course):

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/seq_rename
    </help>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/bioinformatics/btp163</citation>
    </citations>
</tool>