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comparison tools/fasta_tools/fasta_compute_length.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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
34 This 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
40 Suppose 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_
43 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
44 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
45 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
46 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
47
48 Running this tool while setting **How many characters to keep?** to **14** will produce this::
49
50 EYKX4VC02EQLO5 108
51 EYKX4VC02D4GS2 60
52
53
54 </help>
55 </tool>