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comparison fasta_formatter.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fasta_formatter" name="FASTA Width">
2 <description>formatter</description>
3 <!--
4 Note:
5 fasta_formatter also has a tabular output mode (-t),
6 but Galaxy already contains such a tool, so no need
7 to offer the user a duplicated tool.
8
9 So this XML tool only changes the width (line-wrapping) of a
10 FASTA file.
11 -->
12 <command>
13 cat '$input' |
14 fasta_formatter -w $width -o '$output'</command>
15 <inputs>
16 <param format="fasta" name="input" type="data" label="Library to re-format" />
17
18 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line output." />
19 </inputs>
20
21 <tests>
22 <test>
23 <!-- Re-format a FASTA file into a single line -->
24 <param name="input" value="fasta_formatter1.fasta" />
25 <param name="width" value="0" />
26 <output name="output" file="fasta_formatter1.out" />
27 </test>
28 <test>
29 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
30 <param name="input" value="fasta_formatter1.fasta" />
31 <param name="width" value="60" />
32 <output name="output" file="fasta_formatter2.out" />
33 </test>
34 </tests>
35
36 <outputs>
37 <data format="input" name="output" metadata_source="input"
38 />
39 </outputs>
40
41 <help>
42 **What it does**
43
44 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
45
46 **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
47
48 --------
49
50 **Example**
51
52 Input FASTA file (each nucleotides line is 50 characters long)::
53
54 >Scaffold3648
55 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
56 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
57 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
58 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
59 >Scaffold9299
60 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
61 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
62 aactggtctttacctTTAAGTTG
63
64
65 Output FASTA file (with width=80)::
66
67 >Scaffold3648
68 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
69 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
70 ATTTTAATGAACATGTAGTAAAAACT
71 >Scaffold9299
72 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
73 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
74
75 Output FASTA file (with width=0 => single line)::
76
77 >Scaffold3648
78 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
79 >Scaffold9299
80 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
81
82
83 ------
84
85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
86
87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
88 </help>
89 </tool>
90 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->