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author devteam
date Wed, 25 Sep 2013 11:08:42 -0400
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1 <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
2 <description>sequences</description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f '$input' | fastx_collapser -v -o '$output'
7 #if $input.ext == "fastqsanger":
8 -Q 33
9 #end if
10 </command>
11
12 <inputs>
13 <param format="fasta,fastqsanger,fastqsolexa" version="1.0.0" name="input" type="data" label="Library to collapse" />
14 </inputs>
15
16 <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
17 <tests>
18 <test>
19 <param version="1.0.0" name="input" value="fasta_collapser1.fasta" />
20 <output version="1.0.0" name="output" file="fasta_collapser1.out" />
21 </test>
22 </tests>
23 -->
24 <outputs>
25 <data format="fasta" version="1.0.0" name="output" metadata_source="input" />
26 </outputs>
27 <help>
28
29 **What it does**
30
31 This tool collapses identical sequences in a FASTA file into a single sequence.
32
33 --------
34
35 **Example**
36
37 Example Input File (Sequence "ATAT" appears multiple times)::
38
39 >CSHL_2_FC0042AGLLOO_1_1_605_414
40 TGCG
41 >CSHL_2_FC0042AGLLOO_1_1_537_759
42 ATAT
43 >CSHL_2_FC0042AGLLOO_1_1_774_520
44 TGGC
45 >CSHL_2_FC0042AGLLOO_1_1_742_502
46 ATAT
47 >CSHL_2_FC0042AGLLOO_1_1_781_514
48 TGAG
49 >CSHL_2_FC0042AGLLOO_1_1_757_487
50 TTCA
51 >CSHL_2_FC0042AGLLOO_1_1_903_769
52 ATAT
53 >CSHL_2_FC0042AGLLOO_1_1_724_499
54 ATAT
55
56 Example Output file::
57
58 >1-1
59 TGCG
60 >2-4
61 ATAT
62 >3-1
63 TGGC
64 >4-1
65 TGAG
66 >5-1
67 TTCA
68
69 .. class:: infomark
70
71 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
72
73 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
74
75 The following output::
76
77 >2-4
78 ATAT
79
80 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
81
82
83 ------
84
85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
86
87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
88
89 </help>
90 </tool>