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1
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1 <tool id="seq_length" name="Sequence lengths" version="0.0.2">
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2 <description>from FASTA, QUAL, FASTQ, or SFF file</description>
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0
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3 <requirements>
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4 <!-- This is the currently the last release of Biopython which is available via Galaxy's legacy XML packaging system -->
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5 <requirement type="package" version="1.67">biopython</requirement>
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6 </requirements>
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7 <version_command>
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8 python $__tool_directory__/seq_length.py --version
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9 </version_command>
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10 <command detect_errors="aggressive">
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11 python $__tool_directory__/seq_length.py '$input_file' '$input_file.ext' '$output_file'
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12 </command>
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13 <inputs>
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14 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
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15 </inputs>
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16 <outputs>
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17 <data name="output_file" format="tabular" label="${on_string} length"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />
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22 <output name="output_file" file="four_human_proteins.length.tabular" ftype="tabular" />
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23 </test>
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24 <test>
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25 <param name="input_file" value="SRR639755_sample_strict.fastq" ftype="fastq" />
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26 <output name="output_file" file="SRR639755_sample_strict.length.tabular" ftype="tabular" />
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27 </test>
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28 </tests>
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29 <help>
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30 **What it does**
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31
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32 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a
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33 two-column tabular file containing one line per sequence giving the sequence
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34 identifier and the associated sequence's length.
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35
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36 WARNING: If there are any duplicate sequence identifiers, these will all appear
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37 in the tabular output.
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38
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39 **References**
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40
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41 This tool uses Biopython's ``SeqIO`` library to read sequences, so please cite
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42 the Biopython application note (and Galaxy too of course):
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43
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44 Cock et al (2009). Biopython: freely available Python tools for computational
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45 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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46 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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47
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48 This tool is available to install into other Galaxy Instances via the Galaxy
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49 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_length
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50 </help>
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51 <citations>
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52 <citation type="doi">10.1093/bioinformatics/btp163</citation>
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53 </citations>
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54 </tool>
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