Mercurial > repos > devteam > short_reads_figure_high_quality_length
comparison short_reads_figure_high_quality_length.xml @ 0:556ceed24699 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 19 May 2014 12:34:37 -0400 |
| parents | |
| children | 76c4a4ed8e74 |
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| -1:000000000000 | 0:556ceed24699 |
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| 1 <tool id="hist_high_quality_score" name="Histogram" version="1.0.0"> | |
| 2 <description> of high quality score reads </description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.3">rpy</requirement> | |
| 5 <requirement type="package" version="2.11.0">R</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python">short_reads_figure_high_quality_length.py $input1 $output1 $input2</command> | |
| 8 <inputs> | |
| 9 <page> | |
| 10 <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> | |
| 11 <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" /> | |
| 12 </page> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="output1" format="pdf" /> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 <test> | |
| 19 <param name="input1" value="solexa.qual" ftype="qualsolexa" /> | |
| 20 <param name="input2" value="5" /> | |
| 21 <output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/> | |
| 22 </test> | |
| 23 <test> | |
| 24 <param name="input1" value="454.qual" ftype="qual454" /> | |
| 25 <param name="input2" value="5" /> | |
| 26 <output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/> | |
| 27 </test> | |
| 28 </tests> | |
| 29 | |
| 30 <help> | |
| 31 | |
| 32 .. class:: warningmark | |
| 33 | |
| 34 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). | |
| 35 | |
| 36 ----- | |
| 37 | |
| 38 **What it does** | |
| 39 | |
| 40 This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a histogram of lengths of high quality reads. | |
| 41 | |
| 42 ----- | |
| 43 | |
| 44 **Examples of Quality Data** | |
| 45 | |
| 46 Roche (454) or ABI SOLiD data:: | |
| 47 | |
| 48 >seq1 | |
| 49 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 | |
| 50 | |
| 51 Illumina (Solexa) data:: | |
| 52 | |
| 53 -40 -40 40 -40 -40 -40 -40 40 | |
| 54 | |
| 55 ----- | |
| 56 | |
| 57 **Note** | |
| 58 | |
| 59 - Quality score data:: | |
| 60 | |
| 61 >seq1 | |
| 62 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 | |
| 63 | |
| 64 - If the threshold is set to 20: | |
| 65 | |
| 66 - a low quality score 4 in the middle separated two segments of lengths 11 and 5. | |
| 67 | |
| 68 - The histogram will be built based on the numbers (11, 5). | |
| 69 | |
| 70 - For Illumina (Solexa) data, only the maximal of the 4 values will be used. | |
| 71 | |
| 72 | |
| 73 </help> | |
| 74 </tool> |