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