Mercurial > repos > nilesh > rseqc

annotate read_quality.xml @ 53:080fd5739bb4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
author iuc
date Tue, 20 Mar 2018 05:37:48 -0400
parents 34e4c586e3c0
children dbedfc5f5a3c
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_read_quality" name="Read Quality" version="@WRAPPER_VERSION@">
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2 <description>determines Phred quality score</description>
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3
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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements">
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9 <!--
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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10 Required due to conda solver bug: https://github.com/conda/conda/issues/6269
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11 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
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12 -->
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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13 <requirement type="package" version="3.4.1">r-base</requirement>
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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14 </expand>
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16 <expand macro="stdio" />
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18 <version_command><![CDATA[read_quality.py --version]]></version_command>
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20 <command><![CDATA[
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21 read_quality.py
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22 --input-file '${input}'
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23 --out-prefix output
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24 -r ${reduce}
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25 --mapq ${mapq}
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26 ]]>
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27 </command>
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28
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29 <inputs>
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30 <expand macro="bam_sam_param" />
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31 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
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32 <expand macro="mapq_param" />
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33 <expand macro="rscript_output_param" />
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34 </inputs>
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35
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36 <outputs>
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37 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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38 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" />
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39 <expand macro="rscript_output_data" filename="output.qual.r" />
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40 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
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45 <param name="rscript_output" value="true" />
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46 <output name="outputr" file="output.qual.r"/>
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47 <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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48 <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" />
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49 </test>
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50 </tests>
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52 <help><![CDATA[
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53 read_quality.py
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54 +++++++++++++++
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55
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56 According to SAM specification, if Q is the character to represent "base calling quality"
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57 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
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58 returns an integer representing the Unicode code point of the character when the argument
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59 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
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60 to measure "reliability" of base-calling, for example, phred quality score of 20 means
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61 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
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62 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
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63 here P is probability that base-calling is wrong.
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64
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65 Inputs
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66 ++++++++++++++
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67
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68 Input BAM/SAM file
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69 Alignment file in BAM/SAM format.
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70
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71 Ignore phred scores less than this number (default=1000)
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72 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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73
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74 Output
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75 ++++++++++++++
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76
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77 1. output.qual.r
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78 2. output.qual.boxplot.pdf
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79 .. image:: $PATH_TO_IMAGES/36mer.qual.plot.png
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80 :height: 600 px
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81 :width: 600 px
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82 :scale: 80 %
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83 3. output.qual.heatmap.pdf
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84 .. image:: $PATH_TO_IMAGES/36mer.qual.heatmap.png
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85 :height: 600 px
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86 :width: 600 px
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87 :scale: 80 %
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88
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89 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
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90
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91 @ABOUT@
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92
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93 ]]>
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94 </help>
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95
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96 <expand macro="citations" />
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97
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98 </tool>