Mercurial > repos > nilesh > rseqc

annotate junction_annotation.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>compares detected splice junctions to reference gene model</description>
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3 <macros>
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4 <import>rseqc_macros.xml</import>
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5 </macros>
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7 <expand macro="bio_tools"/>
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9 <expand macro="requirements">
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10 <!--
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11 Required due to conda solver bug: https://github.com/conda/conda/issues/6269
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12 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
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13 -->
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14 <requirement type="package" version="4.2.2">r-base</requirement>
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15 </expand>
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17 <expand macro="stdio" />
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19 <version_command><![CDATA[junction_annotation.py --version]]></version_command>
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21 <command><![CDATA[
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22 @BAM_SAM_INPUTS@
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23 junction_annotation.py
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24 --input-file 'input.${extension}'
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25 --refgene '${refgene}'
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26 --out-prefix output
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27 --min-intron ${min_intron}
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28 --mapq ${mapq}
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29 2> >(tee -a stats.txt >&2)
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30 ]]>
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31 </command>
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33 <inputs>
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34 <expand macro="bam_sam_param" />
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35 <expand macro="refgene_param" />
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36 <expand macro="min_intron_param" />
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37 <expand macro="mapq_param" />
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38 <expand macro="rscript_output_param" />
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39 </inputs>
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40
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41 <outputs>
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42 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
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43 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" />
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44 <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" />
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45 <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
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46 <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" />
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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52 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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53 <param name="rscript_output" value="true" />
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54 <output name="outputxls" file="output.junction.xls" ftype="tabular"/>
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55 <output name="outputr" file="output.junction_plot_r" />
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56 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
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57 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
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58 <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" />
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59 </test>
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60 </tests>
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61
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62 <help><![CDATA[
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63 junction_annotation.py
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64 ++++++++++++++++++++++
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66 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
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67 format, this program will compare detected splice junctions to reference gene model. splicing
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68 annotation is performed in two levels: splice event level and splice junction level.
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69
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70 * 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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71 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
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73 All detected junctions can be grouped to 3 exclusive categories:
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74
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75 1. Annotated: The junction is part of the gene model. Both splice sites, 5' splice site
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76 (5'SS) and 3'splice site (3'SS) can be annotated by reference gene model.
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77 2. complete_novel: Complete new junction. Neither of the two splice sites cannot be annotated by gene model
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78 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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80 Inputs
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81 ++++++++++++++
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83 Input BAM/SAM file
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84 Alignment file in BAM/SAM format.
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85
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86 Reference gene model
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87 Gene model in BED format.
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88
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89 Minimum intron length (default=50)
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90 Minimum intron length (bp).
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93 Output
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94 ++++++++++++++
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96 1. output.junc.anno.junction.xls:
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97 - chrom ID
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98 - start position of junction (coordinate is 0 based)
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99 - end position of junction (coordinate is 1 based)
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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100 - number of splice events supporting this junction
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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101 - 'annotated', 'complete_novel' or 'partial_novel'.
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102 2. output.anno.junction_plot.r: R script to generate pie chart
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103 3. output.splice_junction.pdf: plot of splice junctions
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104 4. output.splice_events.pdf: plot of splice events
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105
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106 .. image:: $PATH_TO_IMAGES/junction.png
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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107 :height: 400 px
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108 :width: 850 px
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109 :scale: 80 %
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110
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111 @ABOUT@
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112
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113 ]]>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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114 </help>
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115
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116 <expand macro="citations" />
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117
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118 </tool>