[2] | 1 | <tool id="hist_high_quality_score" name="Histogram"> |
---|
| 2 | <description> of high quality score reads </description> |
---|
| 3 | |
---|
| 4 | <command interpreter="python">short_reads_figure_high_quality_length.py $input1 $output1 $input2</command> |
---|
| 5 | |
---|
| 6 | <inputs> |
---|
| 7 | <page> |
---|
| 8 | <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> |
---|
| 9 | <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" /> |
---|
| 10 | </page> |
---|
| 11 | </inputs> |
---|
| 12 | <outputs> |
---|
| 13 | <data name="output1" format="pdf" /> |
---|
| 14 | </outputs> |
---|
| 15 | <requirements> |
---|
| 16 | <requirement type="python-module">rpy</requirement> |
---|
| 17 | </requirements> |
---|
| 18 | <tests> |
---|
| 19 | <test> |
---|
| 20 | <param name="input1" value="solexa.qual" ftype="qualsolexa" /> |
---|
| 21 | <param name="input2" value="5" /> |
---|
| 22 | <output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/> |
---|
| 23 | </test> |
---|
| 24 | <test> |
---|
| 25 | <param name="input1" value="454.qual" ftype="qual454" /> |
---|
| 26 | <param name="input2" value="5" /> |
---|
| 27 | <output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/> |
---|
| 28 | </test> |
---|
| 29 | </tests> |
---|
| 30 | |
---|
| 31 | <help> |
---|
| 32 | |
---|
| 33 | .. class:: warningmark |
---|
| 34 | |
---|
| 35 | 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). |
---|
| 36 | |
---|
| 37 | ----- |
---|
| 38 | |
---|
| 39 | **What it does** |
---|
| 40 | |
---|
| 41 | 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. |
---|
| 42 | |
---|
| 43 | ----- |
---|
| 44 | |
---|
| 45 | **Examples of Quality Data** |
---|
| 46 | |
---|
| 47 | Roche (454) or ABI SOLiD data:: |
---|
| 48 | |
---|
| 49 | >seq1 |
---|
| 50 | 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 |
---|
| 51 | |
---|
| 52 | Illumina (Solexa) data:: |
---|
| 53 | |
---|
| 54 | -40 -40 40 -40 -40 -40 -40 40 |
---|
| 55 | |
---|
| 56 | ----- |
---|
| 57 | |
---|
| 58 | **Note** |
---|
| 59 | |
---|
| 60 | - Quality score data:: |
---|
| 61 | |
---|
| 62 | >seq1 |
---|
| 63 | 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 |
---|
| 64 | |
---|
| 65 | - If the threshold is set to 20: |
---|
| 66 | |
---|
| 67 | - a low quality score 4 in the middle separated two segments of lengths 11 and 5. |
---|
| 68 | |
---|
| 69 | - The histogram will be built based on the numbers (11, 5). |
---|
| 70 | |
---|
| 71 | - For Illumina (Solexa) data, only the maximal of the 4 values will be used. |
---|
| 72 | |
---|
| 73 | |
---|
| 74 | </help> |
---|
| 75 | </tool> |
---|