Mercurial > repos > devteam > fasta_filter_by_length
annotate fasta_filter_by_length.xml @ 1:c8cd0a03db49 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:13:50 -0500 |
parents | 16679a7f554a |
children | 2fd6033d0e9c |
rev | line source |
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0 | 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"/> | |
1
c8cd0a03db49
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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changeset
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6 <param name="min_length" type="integer" value="0" label="Minimal length" /> |
c8cd0a03db49
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
7 <param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> |
0 | 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> |