Mercurial > repos > xuebing > sharplabtool
comparison tools/fasta_tools/fasta_filter_by_length.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1"> | |
2 <description></description> | |
3 <command interpreter="python">fasta_filter_by_length.py $input $min_length $max_length $output </command> | |
4 <inputs> | |
5 <param name="input" type="data" format="fasta" label="Fasta file"/> | |
6 <param name="min_length" type="integer" size="15" value="0" label="Minimal length" /> | |
7 <param name="max_length" type="integer" size="15" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> | |
8 </inputs> | |
9 <outputs> | |
10 <data name="output" format="fasta"/> | |
11 </outputs> | |
12 <tests> | |
13 <test> | |
14 <param name="input" value="454.fasta" /> | |
15 <param name="min_length" value="10" /> | |
16 <param name="max_length" value="0" /> | |
17 <output name="output" file="fasta_tool_filter_length_1.out" /> | |
18 </test> | |
19 </tests> | |
20 <help> | |
21 | |
22 .. class:: infomark | |
23 | |
24 **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'. | |
25 | |
26 ----- | |
27 | |
28 **What it does** | |
29 | |
30 Outputs sequences between *Minimal length* and *Maximum length*. | |
31 | |
32 ----- | |
33 | |
34 **Example** | |
35 | |
36 Suppose you have the following FASTA formatted sequences:: | |
37 | |
38 >seq1 | |
39 TCATTTAATGAC | |
40 >seq2 | |
41 ATGGC | |
42 >seq3 | |
43 TCACATGATGCCG | |
44 >seq4 | |
45 ATGGAAGC | |
46 | |
47 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp:: | |
48 | |
49 >seq1 | |
50 TCATTTAATGAC | |
51 >seq3 | |
52 TCACATGATGCCG | |
53 | |
54 | |
55 </help> | |
56 </tool> |