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comparison fastq_trimmer.xml @ 0:0b9feb0ed628 draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:32 -0500
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1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0">
2 <description>by column</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements>
6 <command interpreter="python">fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length'</command>
7 <inputs>
8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/>
9 <conditional name="offset_type">
10 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">
11 <option value="offsets_absolute" selected="true">Absolute Values</option>
12 <option value="offsets_percent">Percentage of Read Length</option>
13 </param>
14 <when value="offsets_absolute">
15 <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left">
16 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
17 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
18 </param>
19 <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right">
20 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
21 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
22 </param>
23 </when>
24 <when value="offsets_percent">
25 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float">
26 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>
27 </param>
28 <param name="right_column_offset" label="Offset from 3' end" value="0" type="float">
29 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>
30 </param>
31 </when>
32 </conditional>
33 <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/>
34 </inputs>
35 <outputs>
36 <data name="output_file" format="input" />
37 </outputs>
38 <tests>
39 <test>
40 <!-- Do nothing trim -->
41 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
42 <param name="base_offset_type" value="offsets_absolute"/>
43 <param name="left_column_offset" value="0"/>
44 <param name="right_column_offset" value="0"/>
45 <param name="keep_zero_length" value="keep_zero_length" />
46 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
47 </test>
48 <!-- Trim to empty File -->
49 <test>
50 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
51 <param name="base_offset_type" value="offsets_absolute"/>
52 <param name="left_column_offset" value="30"/>
53 <param name="right_column_offset" value="64"/>
54 <param name="keep_zero_length" value="exclude_zero_length" />
55 <output name="output_file" file="empty_file.dat" />
56 </test>
57 <test>
58 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
59 <param name="base_offset_type" value="offsets_percent"/>
60 <param name="left_column_offset" value="50"/>
61 <param name="right_column_offset" value="50"/>
62 <param name="keep_zero_length" value="exclude_zero_length" />
63 <output name="output_file" file="empty_file.dat" />
64 </test>
65 <!-- Trim to 4 inner-most bases -->
66 <test>
67 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
68 <param name="base_offset_type" value="offsets_absolute"/>
69 <param name="left_column_offset" value="45"/>
70 <param name="right_column_offset" value="45"/>
71 <param name="keep_zero_length" value="exclude_zero_length" />
72 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
73 </test>
74 <test>
75 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
76 <param name="base_offset_type" value="offsets_percent"/>
77 <param name="left_column_offset" value="47.87"/>
78 <param name="right_column_offset" value="47.87"/>
79 <param name="keep_zero_length" value="exclude_zero_length" />
80 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
81 </test>
82 </tests>
83 <help>
84 This tool allows you to trim the ends of reads.
85
86 You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer.
87
88 For example, if you have a read of length 36::
89
90 @Some FASTQ Sanger Read
91 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA
92 +
93 =@@.@;B-%?8&gt;CBA@&gt;7@7BBCA4-48%&lt;;;%&lt;B@
94
95 And you set absolute offsets of 2 and 9::
96
97 @Some FASTQ Sanger Read
98 ATATGTNCTCACTGATAAGTGGATA
99 +
100 @.@;B-%?8&gt;CBA@&gt;7@7BBCA4-4
101
102 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36)::
103
104 @Some FASTQ Sanger Read
105 ATATGTNCTCACTGATAAGTGGATATN
106 +
107 @.@;B-%?8&gt;CBA@&gt;7@7BBCA4-48%
108
109 -----
110
111 .. class:: warningmark
112
113 Trimming a color space read will cause any adapter base to be lost.
114
115 ------
116
117 **Citation**
118
119 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
120
121
122 </help>
123 </tool>