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comparison fastx_uncollapser.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_fastx_uncollapser" name="Uncollapse" version="1.0.0">
2 <description>sequences</description>
3 <command>
4 cat '$input' |
5 fastx_uncollapser -v -o '$output'
6 </command>
7 <inputs>
8 <param format="fasta" name="input" type="data" label="Collapsed FASTA file" />
9 </inputs>
10
11 <tests>
12 <test>
13 <param name="input" value="fasta_uncollapser1.fasta" />
14 <output name="output" file="fasta_uncollapser1.out" />
15 </test>
16 </tests>
17
18 <outputs>
19 <data format="fasta" name="output" metadata_source="input"
20 />
21 </outputs>
22 <help>
23
24 **What it does**
25
26 This tool uncollapses a previously-collapsed FASTA file. It reads each collapsed sequence and generates multiple sequences based on the collapsed read count.
27
28 --------
29
30 **Example**
31
32 Example Input - a collapsed FASTA file (Sequence "ATAT" has four collapsed reads)::
33
34 >1-1
35 TGCG
36 >2-4
37 ATAT
38
39 Example Output - uncollapsed FASTA file (Sequence "ATAT" now appears as 4 separate sequences)::
40
41 >1
42 TGCG
43 >2
44 ATAT
45 >3
46 ATAT
47 >4
48 ATAT
49 >5
50 ATAT
51
52 .. class:: infomark
53
54 The original sequence id (with the read counts) are discarded, with the sequence given a numerical name.
55
56 -----
57
58 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
59
60 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
61
62 </help>
63 </tool>
64 <!-- FASTX-Uncollapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->