Mercurial > repos > peterjc > seq_length
comparison tools/seq_length/seq_length.xml @ 0:c323e29a8248 draft
Initial release v0.0.1
author | peterjc |
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date | Tue, 08 May 2018 09:35:45 -0400 |
parents | |
children | 458f987918a6 |
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1 <tool id="seq_length" name="Sequence lengths" version="0.0.1"> | |
2 <description>with ID mapping from a tabular file</description> | |
3 <requirements> | |
4 <!-- This is the currently the last release of Biopython which is available via Galaxy's legacy XML packaging system --> | |
5 <requirement type="package" version="1.67">biopython</requirement> | |
6 </requirements> | |
7 <version_command> | |
8 python $__tool_directory__/seq_length.py --version | |
9 </version_command> | |
10 <command detect_errors="aggressive"> | |
11 python $__tool_directory__/seq_length.py '$input_file' '$input_file.ext' '$output_file' | |
12 </command> | |
13 <inputs> | |
14 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> | |
15 </inputs> | |
16 <outputs> | |
17 <data name="output_file" format="tabular" label="${on_string} length"/> | |
18 </outputs> | |
19 <tests> | |
20 <test> | |
21 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> | |
22 <output name="output_file" file="four_human_proteins.length.tabular" ftype="tabular" /> | |
23 </test> | |
24 <test> | |
25 <param name="input_file" value="SRR639755_sample_strict.fastq" ftype="fastq" /> | |
26 <output name="output_file" file="SRR639755_sample_strict.length.tabular" ftype="tabular" /> | |
27 </test> | |
28 </tests> | |
29 <help> | |
30 **What it does** | |
31 | |
32 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a | |
33 two-column tabular file containing one line per sequence giving the sequence | |
34 identifier and the associated sequence's length. | |
35 | |
36 WARNING: If there are any duplicate sequence identifiers, these will all appear | |
37 in the tabular output. | |
38 | |
39 **References** | |
40 | |
41 This tool uses Biopython's ``SeqIO`` library to read sequences, so please cite | |
42 the Biopython application note (and Galaxy too of course): | |
43 | |
44 Cock et al (2009). Biopython: freely available Python tools for computational | |
45 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
46 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
47 | |
48 This tool is available to install into other Galaxy Instances via the Galaxy | |
49 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_length | |
50 </help> | |
51 <citations> | |
52 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
53 </citations> | |
54 </tool> |