Mercurial > repos > peterjc > seq_select_by_id
view tools/seq_select_by_id/seq_select_by_id.xml @ 6:91f55ee8fea5 draft
v0.0.11; more tests and assorting minor changes
author | peterjc |
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date | Wed, 13 May 2015 10:56:29 -0400 |
parents | 6842c0c7bc70 |
children | a5602454b0ad |
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<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.62">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_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_source="input_file" metadata_source="input_file" label="Selected sequences from $input_file.name"/> </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" /> <assert_stdout> <has_line line="Indexed 10 sequences" /> <has_line line="Selected 1 sequences by ID" /> </assert_stdout> </test> <!-- this version has white space in the identifier column (id and description) --> <test> <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="k12_hypothetical_alt.tabular" ftype="tabular" /> <param name="column" value="1" /> <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> <assert_stdout> <has_line line="Indexed 10 sequences" /> <has_line line="Selected 1 sequences by ID" /> </assert_stdout> <assert_stderr> <has_line line="WARNING: Some of your identifiers had white space in them, using first word only. e.g.:" /> </assert_stderr> </test> <test expect_failure="true" expect_exit_code="1"> <param name="input_file" value="empty.fasta" ftype="fasta" /> <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> <param name="column" value="1" /> <assert_stdout> <has_line line="Indexed 0 sequences" /> </assert_stdout> <assert_stderr> <has_line line="Identifier 'gi|16127999|ref|NP_414546.1|' not found in sequence file" /> </assert_stderr> </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) 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. **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, write and index sequence 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_select_by_id </help> <citations> <citation type="doi">10.7717/peerj.167</citation> <citation type="doi">10.1093/bioinformatics/btp163</citation> </citations> </tool>