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annotate read_distribution.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_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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8 <expand macro="requirements" />
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[read_distribution.py --version]]></version_command>
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14 <command><![CDATA[
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15 @BAM_SAM_INPUTS@
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16 read_distribution.py -i 'input.${extension}' -r '${refgene}' > '${output}'
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17 ]]>
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18 </command>
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20 <inputs>
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21 <expand macro="bam_sam_param" />
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22 <expand macro="refgene_param" />
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23 </inputs>
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25 <outputs>
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26 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/>
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27 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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32 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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33 <output name="output" file="output.read_distribution.txt"/>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 </test>
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35 </tests>
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37 <help><![CDATA[
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38 read_distribution.py
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39 ++++++++++++++++++++
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41 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped
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42 reads were distributed over genome feature (like CDS exon, 5'UTR exon, 3' UTR exon, Intron,
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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43 Intergenic regions). When genome features are overlapped (e.g. a region could be annotated
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44 as both exon and intron by two different transcripts) , they are prioritize as:
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45 CDS exons > UTR exons > Introns > Intergenic regions, for example, if a read was mapped to
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46 both CDS exon and intron, it will be assigned to CDS exons.
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48 * "Total Reads": This does NOT include those QC fail,duplicate and non-primary hit reads
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49 * "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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50 * "Total Assigned Tags": number of tags that can be unambiguously assigned the 10 groups (see below table).
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51 * 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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52 * When assign tags to genome features, each tag is represented by its middle point.
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54 RSeQC cannot assign those reads that:
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56 * hit to intergenic regions that beyond region starting from TSS upstream 10Kb to TES downstream 10Kb.
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57 * 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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58 * hit to regions covered by both TSS upstream 10Kb and TES downstream 10Kb.
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61 Inputs
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62 ++++++++++++++
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64 Input BAM/SAM file
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65 Alignment file in BAM/SAM format.
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67 Reference gene model
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68 Gene model in BED format.
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70 Sample Output
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73 Output:
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75 =============== ============ =========== ===========
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76 Group Total_bases Tag_count Tags/Kb
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77 =============== ============ =========== ===========
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78 CDS_Exons 33302033 20002271 600.63
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79 5'UTR_Exons 21717577 4408991 203.01
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80 3'UTR_Exons 15347845 3643326 237.38
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81 Introns 1132597354 6325392 5.58
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82 TSS_up_1kb 17957047 215331 11.99
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83 TSS_up_5kb 81621382 392296 4.81
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84 TSS_up_10kb 149730983 769231 5.14
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85 TES_down_1kb 18298543 266161 14.55
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86 TES_down_5kb 78900674 729997 9.25
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87 TES_down_10kb 140361190 896882 6.39
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88 =============== ============ =========== ===========
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90 @ABOUT@
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92 ]]>
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93 </help>
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94
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95 <expand macro="citations" />
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96
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97 </tool>