Mercurial > repos > devteam > fasta_formatter
annotate fasta_formatter.xml @ 1:2cbdd2fc365b
Remove spurious version strings.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 26 Nov 2013 12:42:19 -0500 |
| parents | f7d3b87e9851 |
| children | 61469a8970cd |
| rev | line source |
|---|---|
| 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
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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17 <param format="fasta" name="input" type="data" label="Library to re-format" /> |
| 0 | 18 |
|
1
2cbdd2fc365b
Remove spurious version strings.
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
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
25 <param name="input" value="fasta_formatter1.fasta" /> |
|
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
26 <param name="width" value="0" /> |
|
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
27 <output 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
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
31 <param name="input" value="fasta_formatter1.fasta" /> |
|
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
32 <param name="width" value="60" /> |
|
2cbdd2fc365b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
33 <output name="output" file="fasta_formatter2.out" /> |
| 0 | 34 </test> |
| 35 </tests> | |
| 36 | |
| 37 <outputs> | |
|
1
2cbdd2fc365b
Remove spurious version strings.
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> |