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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 07:24:42 -0500
parents e626b3ff9922
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3:e626b3ff9922 4:8cacfcf96a52
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 &gt;seq1 49 >seq1
51 TCATTTAATGAC 50 TCATTTAATGAC
52 &gt;seq2 51 >seq2
53 ATGGC 52 ATGGC
54 &gt;seq3 53 >seq3
55 TCACATGATGCCG 54 TCACATGATGCCG
56 &gt;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 &gt;seq1 60 >seq1
62 TCATTTAATGAC 61 TCATTTAATGAC
63 &gt;seq3 62 >seq3
64 TCACATGATGCCG 63 TCACATGATGCCG
65 64
66 65
67 </help> 66 ]]></help>
68 </tool> 67 </tool>