Mercurial > repos > lparsons > rseqc

annotate read_quality.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
parents 306127635959
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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1 <tool id="rseqc_read_quality" name="Read Quality" version="2.4galaxy1">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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2 <description>determines Phred quality score</description>
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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4 <macros>
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5 <import>rseqc_macros.xml</import>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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6 </macros>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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8 <requirements>
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9 <expand macro="requirement_package_r" />
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10 <expand macro="requirement_package_numpy" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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11 <expand macro="requirement_package_rseqc" />
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12 </requirements>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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14 <expand macro="stdio" />
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16 <version_command><![CDATA[read_quality.py --version]]></version_command>
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18 <command><![CDATA[
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19 read_quality.py
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20 --input-file $input
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21 --out-prefix output
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22 -r $reduce
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23 --mapq $mapq
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24 ]]>
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25 </command>
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26
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27 <inputs>
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28 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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29 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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30 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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31 </inputs>
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33 <outputs>
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34 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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35 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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36 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
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37 </outputs>
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39 <!-- Unable to succefully run this script with test data
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40 <tests>
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41 <test>
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42 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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43 <output name="outputr" file="output.qual.r"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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44 <output name="outputheatpdf" file="output.qual.heatmap.pdf"/>
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45 <output name="outputboxpdf" file="output.qual.boxplot.pdf"/>
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46 </test>
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47 </tests>
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48 -->
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50 <help><![CDATA[
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51 read_quality.py
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52 +++++++++++++++
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53
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54 According to SAM specification, if Q is the character to represent "base calling quality"
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55 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
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56 returns an integer representing the Unicode code point of the character when the argument
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57 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
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58 to measure "reliability" of base-calling, for example, phred quality score of 20 means
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59 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
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60 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
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61 here P is probability that base-calling is wrong.
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62
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63 Inputs
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64 ++++++++++++++
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65
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66 Input BAM/SAM file
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67 Alignment file in BAM/SAM format.
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68
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69 Ignore phred scores less than this number (default=1000)
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70 To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'.
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71
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72 Output
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73 ++++++++++++++
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75 1. output.qual.r
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76 2. output.qual.boxplot.pdf
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77 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
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78 :height: 600 px
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79 :width: 600 px
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80 :scale: 80 %
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81 3. output.qual.heatmap.pdf
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82 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
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83 :height: 600 px
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84 :width: 600 px
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85 :scale: 80 %
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86
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87 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
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89 -----
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90
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91 About RSeQC
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92 +++++++++++
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94 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
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95
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96 The RSeQC package is licensed under the GNU GPL v3 license.
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97
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98 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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99
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100 .. _RSeQC: http://rseqc.sourceforge.net/
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101 ]]>
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102 </help>
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103
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104 <expand macro="citations" />
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105
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106 </tool>