root/galaxy-central/tools/fastx_toolkit/fastx_collapser.xml

リビジョン 2, 1.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="cshl_fastx_collapser" name="Collapse">
2        <description>sequences</description>
3        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4        <command>zcat -f '$input' | fastx_collapser -v -o '$output' </command>
5
6        <inputs>
7                <param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" />
8        </inputs>
9
10    <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
11        <tests>
12                <test>
13                        <param name="input" value="fasta_collapser1.fasta" />
14                        <output name="output" file="fasta_collapser1.out" />
15                </test>
16        </tests>
17    -->
18        <outputs>
19                <data format="fasta" name="output" metadata_source="input" />
20        </outputs>
21  <help>
22
23**What it does**
24
25This tool collapses identical sequences in a FASTA file into a single sequence.
26
27--------
28
29**Example**
30
31Example Input File (Sequence "ATAT" appears multiple times)::
32
33    >CSHL_2_FC0042AGLLOO_1_1_605_414
34    TGCG
35    >CSHL_2_FC0042AGLLOO_1_1_537_759
36    ATAT
37    >CSHL_2_FC0042AGLLOO_1_1_774_520
38    TGGC
39    >CSHL_2_FC0042AGLLOO_1_1_742_502
40    ATAT
41    >CSHL_2_FC0042AGLLOO_1_1_781_514
42    TGAG
43    >CSHL_2_FC0042AGLLOO_1_1_757_487
44    TTCA
45    >CSHL_2_FC0042AGLLOO_1_1_903_769
46    ATAT
47    >CSHL_2_FC0042AGLLOO_1_1_724_499
48    ATAT
49
50Example Output file::
51
52    >1-1
53    TGCG
54    >2-4
55    ATAT
56    >3-1
57    TGGC
58    >4-1
59    TGAG
60    >5-1
61    TTCA
62   
63.. class:: infomark
64
65Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
66
67The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
68
69The following output::
70
71    >2-4
72    ATAT
73
74means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
75
76</help>
77</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。