Mercurial > repos > devteam > fasta_filter_by_length
comparison fasta_filter_by_length.xml @ 4:8cacfcf96a52 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author | devteam |
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date | Sun, 01 Mar 2020 07:24:42 -0500 |
parents | e626b3ff9922 |
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3:e626b3ff9922 | 4:8cacfcf96a52 |
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1 <tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1"> | 1 <tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.2" profile="16.04"> |
2 <description></description> | 2 <description></description> |
3 <command> | 3 <requirements> |
4 python $__tool_directory__/fasta_filter_by_length.py | 4 <requirement type="package" version="3.7">python</requirement> |
5 '$input' | 5 </requirements> |
6 $min_length | 6 <command> |
7 $max_length | 7 python '$__tool_directory__/fasta_filter_by_length.py' '$input' $min_length $max_length '$output' |
8 '$output' | 8 </command> |
9 </command> | 9 <inputs> |
10 <inputs> | 10 <param name="input" type="data" format="fasta" label="Fasta file"/> |
11 <param name="input" type="data" format="fasta" label="Fasta file"/> | 11 <param name="min_length" type="integer" value="0" label="Minimal length" /> |
12 <param name="min_length" type="integer" value="0" label="Minimal length" /> | 12 <param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> |
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'"/> | 13 </inputs> |
14 </inputs> | 14 <outputs> |
15 <outputs> | 15 <data name="output" format="fasta"/> |
16 <data name="output" format="fasta"/> | 16 </outputs> |
17 </outputs> | 17 <tests> |
18 <tests> | 18 <test> |
19 <test> | 19 <param name="input" value="454.fasta" /> |
20 <param name="input" value="454.fasta" /> | 20 <param name="min_length" value="10" /> |
21 <param name="min_length" value="10" /> | 21 <param name="max_length" value="0" /> |
22 <param name="max_length" value="0" /> | 22 <output name="output" file="fasta_tool_filter_length_1.out" /> |
23 <output name="output" file="fasta_tool_filter_length_1.out" /> | 23 </test> |
24 </test> | 24 <test> |
25 <test> | 25 <param name="input" value="4.fasta" /> |
26 <param name="input" value="4.fasta" /> | 26 <param name="min_length" value="0" /> |
27 <param name="min_length" value="0" /> | 27 <param name="max_length" value="60" /> |
28 <param name="max_length" value="60" /> | 28 <output name="output" file="fasta_tool_filter_length_2.out" /> |
29 <output name="output" file="fasta_tool_filter_length_2.out" /> | 29 </test> |
30 </test> | 30 </tests> |
31 </tests> | 31 <help><![CDATA[ |
32 <help> | |
33 | 32 |
34 .. class:: infomark | 33 .. class:: infomark |
35 | 34 |
36 **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'. | 35 **TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'. |
37 | 36 |
38 ----- | 37 ----- |
39 | 38 |
40 **What it does** | 39 **What it does** |
41 | 40 |
42 Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. | 41 Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. |
43 | 42 |
44 ----- | 43 ----- |
45 | 44 |
46 **Example** | 45 **Example** |
47 | 46 |
48 Suppose you have the following FASTA formatted sequences:: | 47 Suppose you have the following FASTA formatted sequences:: |
49 | 48 |
50 >seq1 | 49 >seq1 |
51 TCATTTAATGAC | 50 TCATTTAATGAC |
52 >seq2 | 51 >seq2 |
53 ATGGC | 52 ATGGC |
54 >seq3 | 53 >seq3 |
55 TCACATGATGCCG | 54 TCACATGATGCCG |
56 >seq4 | 55 >seq4 |
57 ATGGAAGC | 56 ATGGAAGC |
58 | 57 |
59 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp:: | 58 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp:: |
60 | 59 |
61 >seq1 | 60 >seq1 |
62 TCATTTAATGAC | 61 TCATTTAATGAC |
63 >seq3 | 62 >seq3 |
64 TCACATGATGCCG | 63 TCACATGATGCCG |
65 | 64 |
66 | 65 |
67 </help> | 66 ]]></help> |
68 </tool> | 67 </tool> |