Mercurial > repos > peterjc > seq_length
view tools/seq_length/seq_length.xml @ 2:6f29bb9960ac draft
v0.0.3 - Fixed SFF; more tests
author | peterjc |
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date | Mon, 14 May 2018 12:09:50 -0400 |
parents | 458f987918a6 |
children | fcdf11fb34de |
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<tool id="seq_length" name="Sequence lengths" version="0.0.3"> <description>from FASTA, QUAL, FASTQ, or SFF file</description> <requirements> <!-- This is the currently the last release of Biopython which is available via Galaxy's legacy XML packaging system --> <requirement type="package" version="1.67">biopython</requirement> </requirements> <version_command> python $__tool_directory__/seq_length.py --version </version_command> <command detect_errors="aggressive"> python $__tool_directory__/seq_length.py -i '$input_file' -f '$input_file.ext' -o '$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." /> </inputs> <outputs> <data name="output_file" format="tabular" label="${on_string} length"/> </outputs> <tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <output name="output_file" file="four_human_proteins.length.tabular" ftype="tabular" /> <assert_stdout> <has_line line="4 sequences, total length 3297" /> </assert_stdout> </test> <test> <param name="input_file" value="SRR639755_sample_strict.fastq" ftype="fastq" /> <output name="output_file" file="SRR639755_sample_strict.length.tabular" ftype="tabular" /> <assert_stdout> <has_line line="2 sequences, total length 202" /> </assert_stdout> </test> <test> <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> <output name="output_file" file="MID4_GLZRM4E04_rnd30.length.tabular" ftype="tabular" /> <assert_stdout> <has_line line="30 sequences, total length 7504" /> </assert_stdout> </test> </tests> <help> **What it does** Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a two-column tabular file containing one line per sequence giving the sequence identifier and the associated sequence's length. WARNING: If there are any duplicate sequence identifiers, these will all appear in the tabular output. **References** This tool uses Biopython's ``SeqIO`` library to read sequences, so 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. 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_length </help> <citations> <citation type="doi">10.1093/bioinformatics/btp163</citation> </citations> </tool>