Mercurial > repos > devteam > fasta_formatter
annotate fasta_formatter.xml @ 1:1dbb5181c327
Removed excess version attributes.
author | Dave Bouvier <dave@bx.psu.edu> |
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date | Tue, 03 Dec 2013 12:36:12 -0500 |
parents | 8f0ae92440b8 |
children | 9457a20156db |
rev | line source |
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0 | 1 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> |
2 <description>formatter</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
5 </requirements> | |
6 <!-- | |
7 Note: | |
8 fasta_formatter also has a tabular output mode (-t), | |
9 but Galaxy already contains such a tool, so no need | |
10 to offer the user a duplicated tool. | |
11 | |
12 So this XML tool only changes the width (line-wrapping) of a | |
13 FASTA file. | |
14 --> | |
15 <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command> | |
16 <inputs> | |
1
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
17 <param format="fasta" name="input" type="data" label="Library to re-format" /> |
0 | 18 |
1
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
19 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> |
0 | 20 </inputs> |
21 | |
22 <tests> | |
23 <test> | |
24 <!-- Re-format a FASTA file into a single line --> | |
1
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
25 <param name="input" value="fasta_formatter1.fasta" /> |
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
26 <param name="width" value="0" /> |
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
27 <param name="output" file="fasta_formatter1.out" /> |
0 | 28 </test> |
29 <test> | |
30 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> | |
1
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
31 <param name="input" value="fasta_formatter1.fasta" /> |
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
32 <param name="width" value="60" /> |
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
33 <param name="output" file="fasta_formatter2.out" /> |
0 | 34 </test> |
35 </tests> | |
36 | |
37 <outputs> | |
1
1dbb5181c327
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
38 <data format="input" name="output" metadata_source="input" /> |
0 | 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 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
85 | |
86 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
87 | |
88 </help> | |
89 </tool> |