annotate junction_annotation.xml @ 51:09846d5169fa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
parents 6b33e31bda10
children 34e4c586e3c0
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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_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@">
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2 <description>compares detected splice junctions to reference gene model</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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7
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8 <expand macro="requirements" />
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[junction_annotation.py --version]]></version_command>
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14 <command><![CDATA[
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15 junction_annotation.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}
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20 --mapq ${mapq}
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21 ]]>
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22 </command>
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23
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24 <inputs>
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25 <expand macro="bam_sam_param" />
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26 <expand macro="refgene_param" />
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27 <expand macro="min_intron_param" />
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28 <expand macro="mapq_param" />
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29 <expand macro="rscript_output_param" />
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30 </inputs>
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31
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32 <outputs>
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33 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/>
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34 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" />
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35 <expand macro="xls_output_data" filename="output.junction.xls" />
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36 <expand macro="rscript_output_data" filename="output.junction_plot.r" />
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37 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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42 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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43 <param name="rscript_output" value="true" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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44 <output name="outputxls" file="output.junction.xls" />
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45 <output name="outputr" file="output.junction_plot.r" />
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46 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
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47 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
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48 </test>
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49 </tests>
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51 <help><![CDATA[
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52 junction_annotation.py
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53 ++++++++++++++++++++++
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54
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55 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
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56 format, this program will compare detected splice junctions to reference gene model. splicing
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57 annotation is performed in two levels: splice event level and splice junction level.
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58
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59 * splice event: An RNA read, especially long read, can be spliced 2 or more times, each time is called a splicing event; In this sense, 100 spliced reads can produce >= 100 splicing events.
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60 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
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61
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62 All detected junctions can be grouped to 3 exclusive categories:
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63
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64 1. Annotated: The junction is part of the gene model. Both splice sites, 5' splice site
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65 (5'SS) and 3'splice site (3'SS) can be annotated by reference gene model.
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66 2. complete_novel: Complete new junction. Neither of the two splice sites cannot be annotated by gene model
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67 3. partial_novel: One of the splice site (5'SS or 3'SS) is new, while the other splice site is annotated (known)
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68
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69 Inputs
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70 ++++++++++++++
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71
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72 Input BAM/SAM file
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73 Alignment file in BAM/SAM format.
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74
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75 Reference gene model
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76 Gene model in BED format.
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77
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78 Minimum intron length (default=50)
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79 Minimum intron length (bp).
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82 Output
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83 ++++++++++++++
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84
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85 1. output.junc.anno.junction.xls:
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86 - chrom ID
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87 - start position of junction (coordinate is 0 based)
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88 - end position of junction (coordinate is 1 based)
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89 - number of splice events supporting this junction
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90 - 'annotated', 'complete_novel' or 'partial_novel'.
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91 2. output.anno.junction_plot.r: R script to generate pie chart
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92 3. output.splice_junction.pdf: plot of splice junctions
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93 4. output.splice_events.pdf: plot of splice events
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94
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95 .. image:: $PATH_TO_IMAGES/junction.png
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96 :height: 400 px
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97 :width: 850 px
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98 :scale: 80 %
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99
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100 @ABOUT@
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101
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102 ]]>
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103 </help>
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104
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105 <expand macro="citations" />
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106
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107 </tool>