Mercurial > repos > nilesh > rseqc

annotate read_quality.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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1 <tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>determines Phred quality score</description>
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3 <expand macro="bio_tools"/>
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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 <!--
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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="4.2.2">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 @BAM_SAM_INPUTS@
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22 read_quality.py
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23 --input-file 'input.${extension}'
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24 --out-prefix output
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25 -r ${reduce}
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26 --mapq ${mapq}
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27 ]]>
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28 </command>
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29
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30 <inputs>
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31 <expand macro="bam_sam_param" />
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32 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
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33 <expand macro="mapq_param" />
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34 <expand macro="rscript_output_param" />
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35 </inputs>
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36
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37 <outputs>
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38 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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39 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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40 <expand macro="rscript_output_data" filename="output.qual.r" />
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41 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
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46 <param name="rscript_output" value="true" />
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47 <output name="outputr" file="output.qual_r"/>
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48 <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" />
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49 <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" />
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50 </test>
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51 </tests>
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53 <help><![CDATA[
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54 read_quality.py
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55 +++++++++++++++
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56
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57 According to SAM specification, if Q is the character to represent "base calling quality"
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58 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
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59 returns an integer representing the Unicode code point of the character when the argument
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60 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
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61 to measure "reliability" of base-calling, for example, phred quality score of 20 means
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62 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
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63 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
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64 here P is probability that base-calling is wrong.
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65
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66 Inputs
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67 ++++++++++++++
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68
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69 Input BAM/SAM file
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70 Alignment file in BAM/SAM format.
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71
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72 Ignore phred scores less than this number (default=1000)
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73 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
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75 Output
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76 ++++++++++++++
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77
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78 1. output.qual.r
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79 2. output.qual.boxplot.pdf
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80 .. image:: $PATH_TO_IMAGES/36mer.qual.plot.png
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81 :height: 600 px
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82 :width: 600 px
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83 :scale: 80 %
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84 3. output.qual.heatmap.pdf
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85 .. image:: $PATH_TO_IMAGES/36mer.qual.heatmap.png
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86 :height: 600 px
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87 :width: 600 px
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88 :scale: 80 %
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89
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90 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
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91
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92 @ABOUT@
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93
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94 ]]>
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95 </help>
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96
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97 <expand macro="citations" />
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98
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99 </tool>