root/galaxy-central/tools/fastq/fastq_trimmer.xml

リビジョン 2, 5.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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>
81This tool allows you to trim the ends of reads.
82
83You 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
85For 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 
92And 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 
99Or 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
110Trimming a color space read will cause any adapter base to be lost.
111
112  </help>
113</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。