Mercurial > repos > nilesh > rseqc

annotate read_quality.xml @ 10:c63fbdcc0dbe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 20:46:57 +0000
parents caaa120457bc
children d7f6b3653d84
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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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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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8 <expand macro="requirements">
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9 <!--
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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 -->
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13 <requirement type="package" version="3.4.1">r-base</requirement>
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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 ${mapq}
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26 ]]>
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27 </command>
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29 <inputs>
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30 <expand macro="bam_sam_param" />
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31 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
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32 <expand macro="mapq_param" />
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33 <expand macro="rscript_output_param" />
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34 </inputs>
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35
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36 <outputs>
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37 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
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38 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${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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41
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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" />
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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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51
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52 <help><![CDATA[
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53 read_quality.py
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54 +++++++++++++++
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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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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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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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74 Output
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75 ++++++++++++++
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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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93 ]]>
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94 </help>
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96 <expand macro="citations" />
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97
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98 </tool>