Mercurial > repos > peterjc > seq_composition
annotate tools/seq_composition/seq_composition.xml @ 3:7a26bb458806 draft
v0.0.4 using Biopython 1.67 via Tool Shed or (Bio)Conda
author | peterjc |
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date | Wed, 10 May 2017 13:03:42 -0400 |
parents | 4283011f4be2 |
children | 13be788233da |
rev | line source |
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3
7a26bb458806
v0.0.4 using Biopython 1.67 via Tool Shed or (Bio)Conda
peterjc
parents:
2
diff
changeset
|
1 <tool id="seq_composition" name="Sequence composition" version="0.0.4"> |
0 | 2 <description>Count bases or amino-acids</description> |
3 <requirements> | |
3
7a26bb458806
v0.0.4 using Biopython 1.67 via Tool Shed or (Bio)Conda
peterjc
parents:
2
diff
changeset
|
4 <requirement type="package" version="1.67">biopython</requirement> |
0 | 5 </requirements> |
1 | 6 <stdio> |
7 <!-- Anything other than zero is an error --> | |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 </stdio> | |
0 | 11 <version_command interpreter="python">seq_composition.py --version</version_command> |
12 <command interpreter="python"> | |
13 seq_composition.py -o "$output_file" | |
14 ##For loop over inputs | |
15 #for i in $input_file | |
16 --$i.ext "${i}" | |
17 #end for | |
18 </command> | |
19 <inputs> | |
20 <param name="input_file" type="data" format="fasta,fastq,sff" multiple="true" label="Sequence file" help="FASTA, FASTQ, or SFF format." /> | |
21 </inputs> | |
22 <outputs> | |
23 <data name="output_file" format="tabular" label="Sequence composition ${on_string}"/> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> | |
28 <output name="output_file" file="four_human_proteins.seq_composition.tabular" ftype="tabular" /> | |
29 </test> | |
30 <test> | |
31 <param name="input_file" value="ecoli.fastq" ftype="fastq" /> | |
32 <output name="output_file" file="ecoli.seq_composition.tabular" ftype="tabular" /> | |
33 </test> | |
34 <test> | |
35 <param name="input_file" value="ecoli.fastq" ftype="fastqsanger" /> | |
36 <output name="output_file" file="ecoli.seq_composition.tabular" ftype="tabular" /> | |
37 </test> | |
38 <test> | |
39 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | |
40 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular" ftype="tabular"/> | |
41 </test> | |
42 </tests> | |
43 <help> | |
44 **What it does** | |
45 | |
46 Takes input files of sequences (typically FASTA or FASTQ, but also | |
47 Standard Flowgram Format (SFF) is supported), counts all the letters | |
48 in each sequence, and returns a summary table of their counts and | |
49 percentages. | |
50 | |
51 **Citation** | |
52 | |
53 This tool uses Biopython, so if you use this Galaxy tool in work leading to a | |
54 scientific publication please cite the following paper: | |
55 | |
56 Cock et al (2009). Biopython: freely available Python tools for computational | |
57 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
58 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
59 | |
60 This tool is available to install into other Galaxy Instances via the Galaxy | |
61 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_composition | |
62 </help> | |
63 <citations> | |
64 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
65 </citations> | |
66 </tool> |