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annotate fastq_quality_boxplot.xml @ 4:439eed933bf9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:49:29 -0400
parents cd82df766cab
children 5a28b303e432
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439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1">
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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2 <description></description>
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iuc
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3 <macros>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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4 <import>macros.xml</import>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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5 </macros>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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6 <expand macro="requirements" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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9 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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10 fastq_quality_boxplot_graph.sh
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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11 -t '$escaped_element_identifier'
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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12 -i '$input'
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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13 -o '$output'
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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14 ]]></command>
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439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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16 <inputs>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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17 <param name="input" type="data" format="txt" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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18 </inputs>
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19
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439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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20 <outputs>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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21 <data name="output" format="png" metadata_source="input" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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22 </outputs>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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23 <tests>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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24 <test>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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25 <param name="input" value="fastq_quality_boxplot-in1.fastq" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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26 <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="768" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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27 </test>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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28 </tests>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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29 <help><![CDATA[
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30 **What it does**
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31
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32 Creates a boxplot graph for the quality scores in the library.
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33
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34 .. class:: infomark
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35
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36 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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37
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38 -----
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39
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40 **Output Examples**
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41
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42 * Black horizontal lines are medians
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43 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
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44 * Whiskers show outlier at max. 1.5*IQR
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45
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46
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47 An excellent quality library (median quality is 40 for almost all 36 cycles):
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48
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Dave Bouvier <dave@bx.psu.edu>
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49 .. image:: fastq_quality_boxplot_1.png
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51
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52 A relatively good quality library (median quality degrades towards later cycles):
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53
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54 .. image:: fastq_quality_boxplot_2.png
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56 A low quality library (median drops quickly):
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57
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58 .. image:: fastq_quality_boxplot_3.png
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60 ------
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61
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62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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63
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64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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65 ]]></help>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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66 <expand macro="citations" />
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67 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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68 </tool>