Mercurial > repos > peterjc > seq_rename
view tools/seq_rename/seq_rename.xml @ 2:7c0642fc57ad draft
Uploaded v0.0.4, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence.
Includes additional tested added in v0.0.3
author | peterjc |
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date | Fri, 11 Oct 2013 04:39:16 -0400 |
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children | e1398f2ba9fe |
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<tool id="seq_rename" name="Rename sequences" version="0.0.4"> <description>with ID mapping from a tabular file</description> <requirements> <requirement type="package" version="1.62">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> <version_commmand interpreter="python">seq_rename.py --version</version_commmand> <command interpreter="python"> seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file </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,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="fasta" label="Renamed ${on_string}"> <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> <change_format> <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> </change_format> </data> </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. 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. **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> </tool>