root/galaxy-central/tools/filters/trimmer.xml

リビジョン 2, 4.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="trimmer" name="Trim" version="0.0.1">
2    <description>leading or trailing characters</description>
3    <command interpreter="python">
4    trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1
5    </command>
6    <inputs>
7        <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
8        <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" />
9        <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/>
10        <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/>
11        <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)">
12            <option selected="true" value="">No</option>
13            <option value="-q">Yes</option>
14        </param>
15        <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed">
16            <option value="62">&gt;</option>
17            <option value="64">@</option>
18            <option value="43">+</option>
19            <option value="60">&lt;</option>
20            <option value="42">*</option>
21            <option value="45">-</option>
22            <option value="61">=</option>
23            <option value="124">|</option>
24            <option value="63">?</option>
25            <option value="36">$</option>
26            <option value="46">.</option>
27            <option value="58">:</option>
28            <option value="38">&amp;</option>
29            <option value="37">%</option>
30            <option value="94">^</option>
31            <option value="35">&#35;</option>
32         </param>   
33    </inputs>
34    <outputs>
35        <data name="out_file1" format="input" metadata_source="input1"/>
36    </outputs>
37    <tests>
38        <test>
39           <param name="input1" value="trimmer_tab_delimited.dat"/>
40           <param name="col" value="0"/>
41           <param name="start" value="1"/>
42           <param name="end" value="13"/>
43           <param name="ignore" value="62"/>
44           <param name="fastq" value="No"/>
45           <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/>
46        </test>
47        <test>
48           <param name="input1" value="trimmer_tab_delimited.dat"/>
49           <param name="col" value="2"/>
50           <param name="start" value="1"/>
51           <param name="end" value="2"/>
52           <param name="ignore" value="62"/>
53           <param name="fastq" value="No"/>
54           <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/>
55        </test>
56
57    </tests>
58
59    <help>
60
61
62**What it does**
63
64Trims specified number of characters from a dataset or its field (if dataset is tab-delimited).
65
66-----
67
68**Example 1**
69
70Trimming this dataset::
71
72  1234567890
73  abcdefghijk
74
75by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce::
76
77  23456
78  bcdef
79
80-----
81
82**Eaxmple 2**
83
84Trimming column 2 of this dataset::
85
86  bcde  12345   fghij   67890
87  fghij 67890   abcde   12345
88
89by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce::
90
91 abcde  234     fghij   67890
92 fghij  789     abcde   12345
93 
94-----
95
96**Trimming FASTQ datasets**
97
98This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset::
99
100  @081017-and-081020:1:1:1715:1759
101  GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
102  +
103  II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&amp;&amp;B
104 
105cab done by setting **Remove everything from this position to the end** to 31::
106
107  @081017-and-081020:1:1:1715:1759
108  GGACTCAGATAGTAATCCACGCTCCTTTAAA
109  +
110  II#IIIIIII$5+.(9IIIIIII$%*$G$A3
111 
112**Note** that headers are skipped.
113
114.. class:: warningmark
115
116**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example.
117
118
119    </help>
120</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。