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comparison tools/fastq/fastq_trimmer.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0">
2 <description>by column</description>
3 <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>
4 <inputs>
5 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/>
6 <conditional name="offset_type">
7 <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)">
8 <option value="offsets_absolute" selected="true">Absolute Values</option>
9 <option value="offsets_percent">Percentage of Read Length</option>
10 </param>
11 <when value="offsets_absolute">
12 <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left">
13 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
14 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
15 </param>
16 <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right">
17 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
18 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
19 </param>
20 </when>
21 <when value="offsets_percent">
22 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float">
23 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>
24 </param>
25 <param name="right_column_offset" label="Offset from 3' 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 </when>
29 </conditional>
30 <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/>
31 </inputs>
32 <outputs>
33 <data name="output_file" format="input" />
34 </outputs>
35 <tests>
36 <test>
37 <!-- Do nothing trim -->
38 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
39 <param name="base_offset_type" value="offsets_absolute"/>
40 <param name="left_column_offset" value="0"/>
41 <param name="right_column_offset" value="0"/>
42 <param name="keep_zero_length" value="keep_zero_length" />
43 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
44 </test>
45 <!-- Trim to empty File -->
46 <test>
47 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
48 <param name="base_offset_type" value="offsets_absolute"/>
49 <param name="left_column_offset" value="30"/>
50 <param name="right_column_offset" value="64"/>
51 <param name="keep_zero_length" value="exclude_zero_length" />
52 <output name="output_file" file="empty_file.dat" />
53 </test>
54 <test>
55 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
56 <param name="base_offset_type" value="offsets_percent"/>
57 <param name="left_column_offset" value="50"/>
58 <param name="right_column_offset" value="50"/>
59 <param name="keep_zero_length" value="exclude_zero_length" />
60 <output name="output_file" file="empty_file.dat" />
61 </test>
62 <!-- Trim to 4 inner-most bases -->
63 <test>
64 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
65 <param name="base_offset_type" value="offsets_absolute"/>
66 <param name="left_column_offset" value="45"/>
67 <param name="right_column_offset" value="45"/>
68 <param name="keep_zero_length" value="exclude_zero_length" />
69 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
70 </test>
71 <test>
72 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
73 <param name="base_offset_type" value="offsets_percent"/>
74 <param name="left_column_offset" value="47.87"/>
75 <param name="right_column_offset" value="47.87"/>
76 <param name="keep_zero_length" value="exclude_zero_length" />
77 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
78 </test>
79 </tests>
80 <help>
81 This tool allows you to trim the ends of reads.
82
83 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.
84
85 For example, if you have a read of length 36::
86
87 @Some FASTQ Sanger Read
88 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA
89 +
90 =@@.@;B-%?8&gt;CBA@&gt;7@7BBCA4-48%&lt;;;%&lt;B@
91
92 And you set absolute offsets of 2 and 9::
93
94 @Some FASTQ Sanger Read
95 ATATGTNCTCACTGATAAGTGGATA
96 +
97 @.@;B-%?8&gt;CBA@&gt;7@7BBCA4-4
98
99 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36)::
100
101 @Some FASTQ Sanger Read
102 ATATGTNCTCACTGATAAGTGGATATN
103 +
104 @.@;B-%?8&gt;CBA@&gt;7@7BBCA4-48%
105
106 -----
107
108 .. class:: warningmark
109
110 Trimming a color space read will cause any adapter base to be lost.
111
112 ------
113
114 **Citation**
115
116 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;`_
117
118
119 </help>
120 </tool>