/tools/metag_tools/short_reads_trim_seq.xml
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1<tool id="trim_reads" name="Select high quality segments" version="1.0.0">
2<description>from short reads</description>
3
4<command interpreter="python">
5 short_reads_trim_seq.py $trim $length $output1 $input1 $input2 $sequencing_method_choice.input3
6</command>
7<inputs>
8<page>
9 <param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" />
10 <param name="input2" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality scores" />
11 <param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
12 <param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
13 <conditional name="sequencing_method_choice">
14 <param name="sequencer" type="select" label="Select technology">
15 <option value="454">Roche (454) or ABI SOLiD</option>
16 <option value="Solexa">Illumina (Solexa)</option>
17 </param>
18 <when value="454">
19 <param name="input3" type="select" label="Low quality bases in homopolymers" help="if set to 'DO NOT trigger splitting' the program will not count low quality bases that are within or adjacent to homonucleotide runs. This will significantly reduce fragmentation of 454 data">
20 <option value="yes">DO NOT trigger splitting </option>
21 <option value="no">trigger splitting</option>
22 </param>
23 </when>
24 <when value="Solexa">
25 <param name="input3" type="integer" size="5" value="0" label="Restrict length of each read to" help="('0' = do not trim) The quality of Solexa reads drops towards the end. This option allows selecting the specified number of nucleotides from the beginning and then running the tool." />
26 </when>
27 </conditional>
28</page>
29</inputs>
30
31<outputs>
32 <data name="output1" format="fasta" />
33</outputs>
34
35<tests>
36 <test>
37 <param name="sequencer" value="454" />
38 <param name="input1" value="454.fasta" ftype="fasta" />
39 <param name="input2" value="454.qual" ftype="qual454" />
40 <param name="input3" value="no" />
41 <param name="trim" value="20" />
42 <param name="length" value="0" />
43 <output name="output1" file="short_reads_trim_seq_out1.fasta" />
44 </test>
45 <test>
46 <param name="sequencer" value="Solexa" />
47 <param name="input1" value="solexa.fasta" ftype="fasta" />
48 <param name="input2" value="solexa.qual" ftype="qualsolexa" />
49 <param name="input3" value="0" />
50 <param name="trim" value="20" />
51 <param name="length" value="0" />
52 <output name="output1" file="short_reads_trim_seq_out2.fasta" />
53 </test>
54</tests>
55
56<help>
57
58.. class:: warningmark
59
60 To use this tool your quality score dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score*.
61
62-----
63
64**What it does**
65
66This tool finds high quality segments within sequencing reads generated by by Roche (454), Illumina (Solexa), or ABI SOLiD machines.
67
68-----
69
70**Example**
71
72
73Suppose this is your sequencing read::
74
75 5'---------*-------------*------**----3'
76
77where **dashes** (-) are HIGH quality bases (above 20) and **asterisks** (*) are LOW quality bases (below 20). If the **Minimal length of contiguous segment** is set to **5** (of course, only for the purposes of this example), the tool will return::
78
79 5'---------
80 -------------
81 -------
82
83you can see that the tool simply splits the read on low quality bases and then returns all segments longer than 5. **Note**, that the output of this tool will likely contain higher number of shorter sequences compared to the original input. If we set the **Minimal length of contiguous segment** to **0**, the tool will only return the single longest segment::
84
85 -------------
86
87
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89
90
91
92</help>
93</tool>