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1 <tool id="hist_high_quality_score" name="Histogram" version="1.0.0">
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2 <description> of high quality score reads </description>
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3 <requirements>
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4 <requirement type="package" version="1.0.3">rpy</requirement>
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5 <requirement type="package" version="2.11.0">R</requirement>
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6 </requirements>
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7 <command interpreter="python">short_reads_figure_high_quality_length.py $input1 $output1 $input2</command>
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8 <inputs>
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9 <page>
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10 <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
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11 <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" />
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12 </page>
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13 </inputs>
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14 <outputs>
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15 <data name="output1" format="pdf" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input1" value="solexa.qual" ftype="qualsolexa" />
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20 <param name="input2" value="5" />
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21 <output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/>
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22 </test>
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23 <test>
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24 <param name="input1" value="454.qual" ftype="qual454" />
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25 <param name="input2" value="5" />
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26 <output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/>
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27 </test>
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28 </tests>
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29
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30 <help>
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31
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32 .. class:: warningmark
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33
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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).
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35
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36 -----
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37
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38 **What it does**
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39
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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.
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41
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42 -----
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43
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44 **Examples of Quality Data**
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45
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46 Roche (454) or ABI SOLiD data::
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47
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48 >seq1
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49 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
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50
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51 Illumina (Solexa) data::
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52
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53 -40 -40 40 -40 -40 -40 -40 40
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54
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55 -----
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56
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57 **Note**
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58
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59 - Quality score data::
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60
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61 >seq1
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62 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
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63
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64 - If the threshold is set to 20:
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65
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66 - a low quality score 4 in the middle separated two segments of lengths 11 and 5.
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67
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68 - The histogram will be built based on the numbers (11, 5).
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69
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70 - For Illumina (Solexa) data, only the maximal of the 4 values will be used.
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71
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72
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73 </help>
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74 </tool>
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