Mercurial > repos > nilesh > rseqc

annotate junction_saturation.xml @ 54:5873cd7afb67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82
author iuc
date Wed, 13 Jun 2018 18:02:25 -0400
parents 09846d5169fa
children dbedfc5f5a3c
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54
5873cd7afb67 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82
iuc
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1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@.1">
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2 <description>detects splice junctions from each subset and compares them to reference gene model</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
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[junction_saturation.py --version]]></version_command>
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13
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14 <command><![CDATA[
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15 junction_saturation.py
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16 --input-file '${input}'
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17 --refgene '${refgene}'
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18 --out-prefix output
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19 --min-intron ${min_intron}
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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20 --min-coverage ${min_coverage}
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21 --mapq ${mapq}
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22 #if str($percentiles_type.percentiles_type_selector) == "specify":
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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23 --percentile-floor ${percentiles_type.lowBound}
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24 --percentile-ceiling ${percentiles_type.upBound}
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25 --percentile-step ${percentiles_type.percentileStep}
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26 #end if
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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 <expand macro="refgene_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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33 <expand macro="min_intron_param" />
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34 <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)" />
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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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35 <expand macro="mapq_param" />
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36 <conditional name="percentiles_type">
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37 <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency">
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38 <option value="default" selected="true">Default sampling bounds and frequency</option>
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39 <option value="specify">Specify sampling bounds and frequency</option>
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40 </param>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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41 <when value="specify">
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42 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)">
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43 <validator type="in_range" min="0" max="100" />
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44 </param>
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45 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)">
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46 <validator type="in_range" min="0" max="100" />
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47 </param>
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48 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)">
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49 <validator type="in_range" min="0" max="100" />
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50 </param>
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51 </when>
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52 <when value="default"/>
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53 </conditional>
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54 <expand macro="rscript_output_param" />
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55 </inputs>
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56
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57 <outputs>
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58 <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" />
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59 <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" />
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60 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
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66 <param name="rscript_output" value="true" />
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67 <output name="outputr" file="output.junctionSaturation_plot.r" compare="sim_size">
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68 <assert_contents>
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69 <has_line line="pdf('output.junctionSaturation_plot.pdf')" />
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70 <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)" />
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71 </assert_contents>
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72 </output>
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73 <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size" />
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74 </test>
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75 </tests>
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77 <help><![CDATA[
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78 junction_saturation.py
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79 ++++++++++++++++++++++
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80
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81 It's very important to check if current sequencing depth is deep enough to perform
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82 alternative splicing analyses. For a well annotated organism, the number of expressed genes
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83 in particular tissue is almost fixed so the number of splice junctions is also fixed. The fixed
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84 splice junctions can be predetermined from reference gene model. All (annotated) splice
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85 junctions should be rediscovered from a saturated RNA-seq data, otherwise, downstream
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86 alternative splicing analysis is problematic because low abundance splice junctions are
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87 missing. This module checks for saturation by resampling 5%, 10%, 15%, ..., 95% of total
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88 alignments from BAM or SAM file, and then detects splice junctions from each subset and
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89 compares them to reference gene model.
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90
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91 Inputs
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92 ++++++++++++++
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93
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94 Input BAM/SAM file
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95 Alignment file in BAM/SAM format.
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96
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97 Reference gene model
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98 Gene model in BED format.
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99
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100 Sampling Percentiles - Upper Bound, Lower Bound, Sampling Increment (defaults= 100, 5, and 5)
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101 Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment.
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102
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103 Minimum intron length (default=50)
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104 Minimum intron length (bp).
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105
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106 Minimum coverage (default=1)
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107 Minimum number of supportting reads to call a junction.
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108
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109 Output
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110 ++++++++++++++
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111
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112 1. output.junctionSaturation_plot.r: R script to generate plot
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113 2. output.junctionSaturation_plot.pdf
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114
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115 .. image:: $PATH_TO_IMAGES/junction_saturation.png
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116 :height: 600 px
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117 :width: 600 px
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118 :scale: 80 %
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119
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120 In this example, current sequencing depth is almost saturated for "known junction" (red line) detection because the number of "known junction" reaches a plateau. In other words, nearly all "known junctions" (expressed in this particular tissue) have already been detected, and continue sequencing will not detect additional "known junction" and will only increase junction coverage (i.e. junction covered by more reads). While current sequencing depth is not saturated for novel junctions (green).
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121
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122 @ABOUT@
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123
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124 ]]>
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125 </help>
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126
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127 <expand macro="citations" />
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128
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129 </tool>