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comparison fasta_affixer.xml @ 22:58807b35777a draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 11:31:12 +0000
parents c2c69c6090f0
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21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="fasta_affixer" name="FASTA read name affixer" version="1.0.0"> 1 <tool id="fasta_affixer" name="FASTA read name affixer" version="1.0.0.3">
2 <description> Appending suffix and prefix to the read names </description> 2 <description>Appending suffix and prefix to the read names</description>
3 <command interpreter="python3"> 3 <required_files>
4 fasta_affixer.py -f $input -p "$prefix" -s "$suffix" -n $nspace -o $output 4 <include type="literal" path="fasta_affixer.py"/>
5 </command> 5 </required_files>
6 6
7 <inputs> 7 <command>
8 <param format="fasta" type="data" name="input" label="Choose your FASTA file" /> 8 python '$__tool_directory__'/fasta_affixer.py -f $input -p "$prefix" -s "$suffix"
9 <param name="prefix" type="text" size="10" value="" label="Prefix" help="Enter prefix which will be added to all read names" /> 9 -n $nspace -o $output
10 <param name="suffix" type="text" size="10" value="" label="Suffix" help="Enter suffix which will be added to all read names"/> 10 </command>
11 <param name="nspace" type="integer" size="10" value="0" min="0" max="1000" label="Number of spaces in the name to ignore" help="By default, a string before the first space is considered to be the read name, and all characters following the space are discarded. If you want to keep the information following the space(s) in the name, enter positive integer."/> 11
12 </inputs> 12 <inputs>
13 <param format="fasta" type="data" name="input" label="Choose your FASTA file"/>
14 <param name="prefix" type="text" size="10" value="" label="Prefix"
15 help="Enter prefix which will be added to all read names"/>
16 <param name="suffix" type="text" size="10" value="" label="Suffix"
17 help="Enter suffix which will be added to all read names"/>
18 <param name="nspace" type="integer" size="10" value="0" min="0" max="1000"
19 label="Number of spaces in the name to ignore"
20 help="By default, a string before the first space is considered to be the read name, and all characters following the space are discarded. If you want to keep the information following the space(s) in the name, enter positive integer."/>
21 </inputs>
22
23 <outputs>
24 <data format="fasta" name="output"
25 label="FASTA dataset ${input.hid} with modified sequence names"/>
26 </outputs>
27
28 <tests>
29 <test>
30 <param name="input" value="single_output.fasta"/>
31 <param name="prefix" value="TEST"/>
32 <param name="suffux" value="OK"/>
33 <param name="nspace" value="0"/>
34 <output name="output" value="prefix_suffix.fasta"/>
35 </test>
36 </tests>
37 <help>
38 **What is does**
39
40 Tool for appending prefix and suffix to sequences names in fasta formated
41 sequences. This tool is useful
42 if you want to do comparative analysis with RepeatExplorer and need to
43 append sample codes to sequence identifiers
44
45 **Example**
46 The following fasta file:
47
48 ::
49
50 >123454
51 acgtactgactagccatgacg
52 >234235
53 acgtactgactagccatgacg
54
55 is renamed to:
56
57 ::
58
59 >prefix123454suffix
60 acgtactgactagccatgacg
61 >prefix234235suffix
62 acgtactgactagccatgacg
13 63
14 64
15 <outputs> 65 By default, anything after spaces is
16 <data format="fasta" name="output" label="FASTA dataset ${input.hid} with modified sequence names" /> 66 excluded from sequences name. In example sequence:
17 </outputs>
18 67
19 <tests> 68 ::
20 <test>
21 <param name="input" value="single_output.fasta" />
22 <param name="prefix" value="TEST" />
23 <param name="suffux" value="OK"/>
24 <param name="nspace" value="0" />
25 <output name="output" value="prefix_suffix.fasta" />
26 </test>
27 </tests>
28 <help>
29 **What is does**
30
31 Tool for appending prefix and suffix to sequences names in fasta formated sequences. This tool is useful
32 if you want to do comparative analysis with RepeatExplorer and need to
33 append sample codes to sequence identifiers
34 69
35 **Example** 70 >SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
36 The following fasta file: 71 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
72 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
37 73
38 :: 74 when **Number of spaces in name to ignore** is set to 0 (default) the output will
75 be:
39 76
40 >123454 77 ::
41 acgtactgactagccatgacg
42 >234235
43 acgtactgactagccatgacg
44 78
45 is renamed to: 79 >prefixSRR352150.23846180suffix
46 80 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
47 ::
48
49 >prefix123454suffix
50 acgtactgactagccatgacg
51 >prefix234235suffix
52 acgtactgactagccatgacg
53 81
54 82
55 By default, anything after spaces is 83 If you want to keep spaces the setting **Number of spaces in name to ignore** to 1
56 excluded from sequences name. In example sequence: 84 will yield
57 85
58 :: 86 ::
59
60 >SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
61 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
62 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
63 87
64 when **Number of spaces in name to ignore** is set to 0 (default) the output will be: 88 >prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
65 89 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
66 ::
67
68 >prefixSRR352150.23846180suffix
69 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
70
71
72 If you want to keep spaces the setting **Number of spaces in name to ignore** to 1 will yield
73
74 ::
75
76 >prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
77 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
78 90
79 91
80 </help> 92 </help>
81 </tool> 93 </tool>