Mercurial > repos > peterjc > seq_select_by_id
view tools/filters/seq_select_by_id.xml @ 2:28d52478ace9 draft
Uploaded v0.0.4 which adds a unit test.
author | peterjc |
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date | Mon, 15 Apr 2013 12:28:51 -0400 |
parents | 50a8a6917a9c |
children | 19e26966ed3e |
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<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.4"> <description>from a tabular file</description> <version_command interpreter="python">seq_select_by_id.py --version</version_command> <command interpreter="python"> seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file </command> <inputs> <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> </inputs> <outputs> <data name="output_file" format="fasta" label="Selected sequences"> <!-- 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="k12_ten_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> <param name="column" value="1" /> <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> </test> </tests> <requirements> <requirement type="python-module">Bio</requirement> </requirements> <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) containing only the records with identifiers in the tabular file (in the order from the tabular file). WARNING: If you have any duplicates in the tabular file identifiers, you will get duplicate sequences in the output. **Citation** This tool uses Biopython to read, write and index sequence files. If you use this tool in scientific work leading to a publication, please 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. </help> </tool>