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comparison fastx_collapser.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_collapser" name="Collapse">
2 <description>sequences</description>
3 <command>
4 cat '$input' |
5 fastx_collapser
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 -v -o '$output'
12 </command>
13
14 <inputs>
15 <param format="fastq,fastqsanger,fasta" name="input" type="data" label="Library to collapse" />
16 </inputs>
17
18 <tests>
19 <test>
20 <param name="input" value="fasta_collapser1.fasta" />
21 <output name="output" file="fasta_collapser1.out" />
22 </test>
23 </tests>
24
25 <outputs>
26 <data format="fasta" name="output" metadata_source="input"
27 />
28 </outputs>
29 <help>
30
31 **What it does**
32
33 This tool collapses identical sequences in a FASTQ or FASTA file into a single sequence.
34
35 --------
36
37 **Example**
38
39 Example Input File (Sequence "ATAT" appears multiple times)::
40
41 >CSHL_2_FC0042AGLLOO_1_1_605_414
42 TGCG
43 >CSHL_2_FC0042AGLLOO_1_1_537_759
44 ATAT
45 >CSHL_2_FC0042AGLLOO_1_1_774_520
46 TGGC
47 >CSHL_2_FC0042AGLLOO_1_1_742_502
48 ATAT
49 >CSHL_2_FC0042AGLLOO_1_1_781_514
50 TGAG
51 >CSHL_2_FC0042AGLLOO_1_1_757_487
52 TTCA
53 >CSHL_2_FC0042AGLLOO_1_1_903_769
54 ATAT
55 >CSHL_2_FC0042AGLLOO_1_1_724_499
56 ATAT
57
58 Example Output file::
59
60 >1-1
61 TGCG
62 >2-4
63 ATAT
64 >3-1
65 TGGC
66 >4-1
67 TGAG
68 >5-1
69 TTCA
70
71 .. class:: infomark
72
73 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
74
75 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
76
77 The following output::
78
79 >2-4
80 ATAT
81
82 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
83
84 ------
85
86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
87
88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
89
90 </help>
91 </tool>
92 <!-- FASTX-Collapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->