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1 <tool id="trim_reads" name="Select high quality segments" version="1.0.0">
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2 <description></description>
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3
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4 <command interpreter="python">
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5 short_reads_trim_seq.py $trim $length $output1 $input1 $input2 $sequencing_method_choice.input3
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6 </command>
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7 <inputs>
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8 <page>
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9 <param name="input1" type="data" format="fasta" label="Reads" />
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10 <param name="input2" type="data" format="qualsolexa,qual454" label="Quality scores" />
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11 <param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
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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" />
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13 <conditional name="sequencing_method_choice">
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14 <param name="sequencer" type="select" label="Select technology">
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15 <option value="454">Roche (454) or ABI SOLiD</option>
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16 <option value="Solexa">Illumina (Solexa)</option>
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17 </param>
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18 <when value="454">
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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">
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20 <option value="yes">DO NOT trigger splitting </option>
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21 <option value="no">trigger splitting</option>
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22 </param>
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23 </when>
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24 <when value="Solexa">
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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." />
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26 </when>
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27 </conditional>
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28 </page>
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29 </inputs>
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30
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31 <outputs>
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32 <data name="output1" format="fasta" />
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33 </outputs>
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34
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35 <tests>
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36 <test>
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37 <param name="sequencer" value="454" />
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38 <param name="input1" value="454.fasta" ftype="fasta" />
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39 <param name="input2" value="454.qual" ftype="qual454" />
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40 <param name="input3" value="no" />
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41 <param name="trim" value="20" />
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42 <param name="length" value="0" />
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43 <output name="output1" file="short_reads_trim_seq_out1.fasta" />
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44 </test>
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45 <test>
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46 <param name="sequencer" value="Solexa" />
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47 <param name="input1" value="solexa.fasta" ftype="fasta" />
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48 <param name="input2" value="solexa.qual" ftype="qualsolexa" />
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49 <param name="input3" value="0" />
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50 <param name="trim" value="20" />
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51 <param name="length" value="0" />
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52 <output name="output1" file="short_reads_trim_seq_out2.fasta" />
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53 </test>
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54 </tests>
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55
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56 <help>
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57
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58 .. class:: warningmark
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59
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60 To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples).
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61
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62 -----
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63
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64 **What it does**
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65
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66 This tool finds high quality segments within sequencing reads generated by by Roche (454), Illumina (Solexa), or ABI SOLiD machines.
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67
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68 -----
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69
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70 **Example**
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71
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72
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73 Suppose this is your sequencing read::
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74
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75 5'---------*-------------*------**----3'
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76
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77 where **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::
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78
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79 5'---------
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80 -------------
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81 -------
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82
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83 you 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::
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84
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85 -------------
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86
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87
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88
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89
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90
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91
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92 </help>
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93 </tool>
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