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annotate read_distribution.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
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1 <tool id="rseqc_read_distribution" name="Read Distribution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>calculates how mapped reads were distributed over genome feature</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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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <version_command><![CDATA[read_distribution.py --version]]></version_command>
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10 <command><![CDATA[
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11 @BAM_SAM_INPUTS@
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12 read_distribution.py -i 'input.${extension}' -r '${refgene}' > '${output}'
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13 ]]>
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14 </command>
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15 <inputs>
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16 <expand macro="bam_sam_param"/>
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17 <expand macro="refgene_param"/>
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18 </inputs>
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19 <outputs>
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20 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/>
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21 </outputs>
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22 <tests>
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23 <test expect_num_outputs="1">
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24 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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25 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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26 <output name="output" file="output.read_distribution.txt"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 read_distribution.py
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31 ++++++++++++++++++++
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32
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33 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped
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34 reads were distributed over genome feature (like CDS exon, 5'UTR exon, 3' UTR exon, Intron,
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35 Intergenic regions). When genome features are overlapped (e.g. a region could be annotated
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36 as both exon and intron by two different transcripts) , they are prioritize as:
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37 CDS exons > UTR exons > Introns > Intergenic regions, for example, if a read was mapped to
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38 both CDS exon and intron, it will be assigned to CDS exons.
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39
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40 * "Total Reads": This does NOT include those QC fail,duplicate and non-primary hit reads
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41 * "Total Tags": reads spliced once will be counted as 2 tags, reads spliced twice will be counted as 3 tags, etc. And because of this, "Total Tags" >= "Total Reads"
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42 * "Total Assigned Tags": number of tags that can be unambiguously assigned the 10 groups (see below table).
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43 * Tags assigned to "TSS_up_1kb" were also assigned to "TSS_up_5kb" and "TSS_up_10kb", tags assigned to "TSS_up_5kb" were also assigned to "TSS_up_10kb". Therefore, "Total Assigned Tags" = CDS_Exons + 5'UTR_Exons + 3'UTR_Exons + Introns + TSS_up_10kb + TES_down_10kb.
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44 * When assign tags to genome features, each tag is represented by its middle point.
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45
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46 RSeQC cannot assign those reads that:
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48 * hit to intergenic regions that beyond region starting from TSS upstream 10Kb to TES downstream 10Kb.
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49 * hit to regions covered by both 5'UTR and 3' UTR. This is possible when two head-to-tail transcripts are overlapped in UTR regions.
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50 * hit to regions covered by both TSS upstream 10Kb and TES downstream 10Kb.
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53 Inputs
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54 ++++++++++++++
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55
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56 Input BAM/SAM file
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57 Alignment file in BAM/SAM format.
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58
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59 Reference gene model
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60 Gene model in BED format.
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61
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62 Sample Output
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63 ++++++++++++++
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64
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65 Output:
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67 =============== ============ =========== ===========
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68 Group Total_bases Tag_count Tags/Kb
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69 =============== ============ =========== ===========
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70 CDS_Exons 33302033 20002271 600.63
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71 5'UTR_Exons 21717577 4408991 203.01
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72 3'UTR_Exons 15347845 3643326 237.38
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73 Introns 1132597354 6325392 5.58
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74 TSS_up_1kb 17957047 215331 11.99
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75 TSS_up_5kb 81621382 392296 4.81
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76 TSS_up_10kb 149730983 769231 5.14
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77 TES_down_1kb 18298543 266161 14.55
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78 TES_down_5kb 78900674 729997 9.25
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79 TES_down_10kb 140361190 896882 6.39
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80 =============== ============ =========== ===========
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81
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82 @ABOUT@
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83
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84 ]]>
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85 </help>
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86 <expand macro="citations"/>
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87 </tool>