root/galaxy-central/tools/fasta_tools/fasta_compute_length.xml

リビジョン 2, 2.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="fasta_compute_length" name="Compute sequence length">
2        <description></description>
3        <command interpreter="python">fasta_compute_length.py $input $output $keep_first</command>
4        <inputs>
5                <param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
6                <param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
7        </inputs>
8        <outputs>
9                <data name="output" format="tabular"/>
10        </outputs>
11        <tests>
12                <test>
13                        <param name="input" value="454.fasta" />
14                        <param name="keep_first" value="0"/>
15                        <output name="output" file="fasta_tool_compute_length_1.out" />
16                </test>
17               
18                <test>
19                        <param name="input" value="extract_genomic_dna_out1.fasta" />
20                        <param name="keep_first" value="0"/>
21                        <output name="output" file="fasta_tool_compute_length_2.out" />
22                </test>
23               
24                <test>
25                        <param name="input" value="454.fasta" />
26                        <param name="keep_first" value="14"/>
27                        <output name="output" file="fasta_tool_compute_length_3.out" />
28                </test>
29        </tests>
30        <help>
31
32**What it does**
33
34This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
35
36-----   
37
38**Example**
39
40Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
41
42    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_     TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG     TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG     &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_     AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
43
44Running this tool while setting **How many characters to keep?** to **14** will produce this::
45       
46        EYKX4VC02EQLO5  108
47        EYKX4VC02D4GS2   60
48
49
50        </help>
51</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。