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annotate fastq_quality_filter.xml @ 3:43a7370aa010 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:35 -0400
parents e41385662e5e
children 7b4468117008
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43a7370aa010 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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1 <tool id="cshl_fastq_quality_filter" version="1.0.1" name="Filter by quality">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastq_quality_filter
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9 -q $quality
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10 -p $percent
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11 -v
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12 -o '$output'
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13 @FQQUAL@
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14 ]]></command>
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15
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16 <inputs>
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17 <expand macro="fastq_input" />
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18
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19 <param name="quality" type="integer" value="20" label="Quality cut-off value"/>
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20
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21 <param name="percent" type="integer" value="90"
43a7370aa010 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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22 label="Percent of bases in sequence that must have quality equal to / higher than cut-off value" />
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23 </inputs>
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24 <outputs>
3
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25 <data name="output" format_source="input" metadata_source="input" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) -->
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30 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" />
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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31 <param name="quality" value="33"/>
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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32 <param name="percent" value="100"/>
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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33 <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1a.out" />
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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34 </test>
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35 <test>
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36 <!-- Test2: 80% of bases with quality 20 or higher -->
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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37 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/>
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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38 <param name="quality" value="20"/>
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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39 <param name="percent" value="80"/>
e41385662e5e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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40 <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" />
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41 </test>
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42 </tests>
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43 <help><![CDATA[
0
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44 **What it does**
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45
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46 This tool filters reads based on quality scores.
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47
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48 .. class:: infomark
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49
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50 Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value.
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51
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52 .. class:: infomark
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53
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54 Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value.
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55
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56 --------
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57
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58 Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded.
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59
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60
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61 **Example**::
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62
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63 @CSHL_4_FC042AGOOII:1:2:214:584
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64 GACAATAAAC
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65 +CSHL_4_FC042AGOOII:1:2:214:584
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66 30 30 30 30 30 30 30 30 20 10
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67
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68 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30).
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69
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70 Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30).
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71
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72 Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20).
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73
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74 ------
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75
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76 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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77
2
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78 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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79 ]]></help>
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80 <expand macro="citations" />
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81 <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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82 </tool>