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comparison tools/fastx_toolkit/fasta_formatter.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cshl_fasta_formatter" name="FASTA Width">
2 <description>formatter</description>
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4 <!--
5 Note:
6 fasta_formatter also has a tabular output mode (-t),
7 but Galaxy already contains such a tool, so no need
8 to offer the user a duplicated tool.
9
10 So this XML tool only changes the width (line-wrapping) of a
11 FASTA file.
12 -->
13 <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command>
14 <inputs>
15 <param format="fasta" name="input" type="data" label="Library to re-format" />
16
17 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
18 </inputs>
19
20 <tests>
21 <test>
22 <!-- Re-format a FASTA file into a single line -->
23 <param name="input" value="fasta_formatter1.fasta" />
24 <param name="width" value="0" />
25 <output name="output" file="fasta_formatter1.out" />
26 </test>
27 <test>
28 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
29 <param name="input" value="fasta_formatter1.fasta" />
30 <param name="width" value="60" />
31 <output name="output" file="fasta_formatter2.out" />
32 </test>
33 </tests>
34
35 <outputs>
36 <data format="input" name="output" metadata_source="input" />
37 </outputs>
38
39 <help>
40 **What it does**
41
42 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
43
44 **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.
45
46 --------
47
48 **Example**
49
50 Input FASTA file (each nucleotides line is 50 characters long)::
51
52 >Scaffold3648
53 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
54 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
55 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
56 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
57 >Scaffold9299
58 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
59 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
60 aactggtctttacctTTAAGTTG
61
62
63 Output FASTA file (with width=80)::
64
65 >Scaffold3648
66 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
67 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
68 ATTTTAATGAACATGTAGTAAAAACT
69 >Scaffold9299
70 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
71 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
72
73 Output FASTA file (with width=0 => single line)::
74
75 >Scaffold3648
76 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
77 >Scaffold9299
78 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
79 </help>
80 </tool>