Mercurial > repos > devteam > fasta_filter_by_length
annotate fasta_filter_by_length.xml @ 2:2fd6033d0e9c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
author | devteam |
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date | Thu, 20 Jul 2017 13:49:07 -0400 |
parents | c8cd0a03db49 |
children | e626b3ff9922 |
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0 | 1 <tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1"> |
2 <description></description> | |
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2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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3 <command> |
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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4 python $__tool_directory__/fasta_filter_by_length.py |
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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5 '$input' |
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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6 $min_length |
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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7 $max_length |
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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8 '$output' |
2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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9 </command> |
0 | 10 <inputs> |
11 <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
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12 <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
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13 <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 | 14 </inputs> |
15 <outputs> | |
16 <data name="output" format="fasta"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="input" value="454.fasta" /> | |
21 <param name="min_length" value="10" /> | |
22 <param name="max_length" value="0" /> | |
23 <output name="output" file="fasta_tool_filter_length_1.out" /> | |
24 </test> | |
25 </tests> | |
26 <help> | |
27 | |
28 .. class:: infomark | |
29 | |
30 **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'. | |
31 | |
32 ----- | |
33 | |
34 **What it does** | |
35 | |
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2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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36 Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. |
0 | 37 |
38 ----- | |
39 | |
40 **Example** | |
41 | |
42 Suppose you have the following FASTA formatted sequences:: | |
43 | |
44 >seq1 | |
45 TCATTTAATGAC | |
46 >seq2 | |
47 ATGGC | |
48 >seq3 | |
49 TCACATGATGCCG | |
50 >seq4 | |
51 ATGGAAGC | |
52 | |
53 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp:: | |
54 | |
55 >seq1 | |
56 TCATTTAATGAC | |
57 >seq3 | |
58 TCACATGATGCCG | |
59 | |
60 | |
61 </help> | |
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2fd6033d0e9c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit ad697ba869f1a81bb78168d3b81e360996fd2d52
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62 </tool> |