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annotate fastq_quality_filter.xml @ 2:e41385662e5e draft

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author devteam
date Wed, 11 Nov 2015 12:37:55 -0500
parents 57adb07cccfc
children 43a7370aa010
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1 <tool id="cshl_fastq_quality_filter" version="1.0.0" name="Filter by quality">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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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8 zcat -f < '$input' | fastq_quality_filter -q $quality -p $percent -v -o '$output'
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9 #if $input.ext == "fastqsanger":
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10 -Q 33
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11 #end if
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12 ]]>
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13 </command>
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14
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15 <inputs>
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16 <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" />
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17
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18 <param name="quality" type="integer" value="20">
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19 <label>Quality cut-off value</label>
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20 </param>
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21
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22 <param name="percent" type="integer" value="90">
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23 <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format_source="input" name="output" metadata_source="input" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) -->
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32 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" />
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33 <param name="quality" value="33"/>
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34 <param name="percent" value="100"/>
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35 <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1a.out" />
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36 </test>
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37 <test>
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38 <!-- Test2: 80% of bases with quality 20 or higher -->
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39 <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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40 <param name="quality" value="20"/>
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41 <param name="percent" value="80"/>
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42 <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" />
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43 </test>
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44 </tests>
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45 <help>
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46 **What it does**
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47
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48 This tool filters reads based on quality scores.
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49
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50 .. class:: infomark
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51
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52 Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value.
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53
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54 .. class:: infomark
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55
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56 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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57
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58 --------
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59
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60 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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61
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62
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63 **Example**::
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64
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65 @CSHL_4_FC042AGOOII:1:2:214:584
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66 GACAATAAAC
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67 +CSHL_4_FC042AGOOII:1:2:214:584
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68 30 30 30 30 30 30 30 30 20 10
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69
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70 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30).
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71
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72 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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73
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74 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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75
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76 ------
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77
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78 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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79
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80 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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81 </help>
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82 <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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83 </tool>