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annotate short_reads_trim_seq.xml @ 1:ece3c79e81ae draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:31:41 -0400 |
| parents | 8c0b907e6e5b |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="trim_reads" name="Select high quality segments" version="1.0.0"> |
| 2 <description></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" label="Reads" /> | |
| 10 <param name="input2" type="data" format="qualsolexa,qual454" label="Quality scores" /> | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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11 <param name="trim" type="integer" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/> |
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ece3c79e81ae
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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12 <param name="length" type="integer" 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" /> |
| 0 | 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"> | |
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ece3c79e81ae
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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25 <param name="input3" type="integer" 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." /> |
| 0 | 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 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). | |
| 61 | |
| 62 ----- | |
| 63 | |
| 64 **What it does** | |
| 65 | |
| 66 This 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 | |
| 73 Suppose this is your sequencing read:: | |
| 74 | |
| 75 5'---------*-------------*------**----3' | |
| 76 | |
| 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:: | |
| 78 | |
| 79 5'--------- | |
| 80 ------------- | |
| 81 ------- | |
| 82 | |
| 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:: | |
| 84 | |
| 85 ------------- | |
| 86 | |
| 87 | |
| 88 | |
| 89 | |
| 90 | |
| 91 | |
| 92 </help> | |
| 93 </tool> |