Mercurial > repos > rnateam > ribotaper

annotate ribotaper_part2_create_metaplots.xml @ 0:93b90466d533 draft

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author rnateam
date Tue, 07 Jun 2016 17:49:46 -0400
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1 <tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.3.1">ribotaper</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8
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9 <command><![CDATA[
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10 create_metaplots.bash
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11 "$ribo_bam"
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12 "$start_stops_FAR"
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13 "metagene"
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14
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15 &&
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16
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17 find "metaplots"
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18 "-name"
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19 "metagene*.pdf"
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20 | sort | xargs gs
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21 "-dAutoRotatePages=/None"
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22 "-dBATCH"
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23 "-dNOPAUSE"
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24 "-q"
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25 "-sDEVICE=pdfwrite"
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26 "-sOutputFile=merged_metagene.pdf"
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27
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28 ]]></command>
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29 <inputs>
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30 <param name="ribo_bam" type="data" format="bam" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
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31 <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/>
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32 </inputs>
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33 <outputs>
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34 <data name="output1" type="data" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
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35 <data name="output2" type="data" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
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40 <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed" ftype="bed"/>
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41 <output name="output2" file="metagene"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 Overview
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46 --------
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47
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48 RiboTaper is an analysis pipeline for Ribosome Profiling
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49 (Ribo-seq) experiments,
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50 which exploits the triplet periodicity of
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51 ribosomal footprints to call translated regions.
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52 See
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53 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
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54
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55
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56 The Ribotaper Galaxy tool set consists of three tools:
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57
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58 - ``ribotaper part 1``: creation of annotation files
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59 - ``ribotaper part 2``: metagene analysis for P-sites definition
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60 - ``ribotaper part 3``: ribosome profiling
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61
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62 The order of execution should follow:
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63 ``ribotaper part 1, part 2 and part 3``.
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64
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65 The current tool is ``ribotaper part 2``,
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66 metagene analysis for P-sites definition.
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67
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68 Output
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69 --------
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70
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71 ``Ribotaper part 2`` generates two files:
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72
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73 - **Metagene analysis results for P-sites definition** in pdf format
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74 - **Metagene analysis results for P-sites definition** in tablular format
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75
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76 The outputs include the aggregate profiles around the start and stop codons for the 5'-end of different Ribo-seq read lengths.
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77 Deciding which Ribo-seq read length to use at which distance cutoff to define P-sites position is the critical decision for the whole RiboTaper pipeline.
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78 These plots should help you decide which read lengths to use and with which cutoff.
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79 Ideally, the user should pick up the read lengths which show a specific frame preference (same color preference for all the 4 subplots) and a peak around a specific distance on the start codon.
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80 Sometimes a peak at the stop codon is also visible, but often in a different frame. This may have biological relevance, but it is still not very well explained by the community.
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81 As seen in the example, taken from the Ribo-seq data of our publication, the 29 nt reads show a very nice frame preference and a peak of 12 nt distance from the annotated start codons. Which means the 29 nt reads with a 12 distance cutoff can be chosen.
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82 Usually reads around 29 nt with 12 nt distance cutoff are the outcome of many Ribo-seq experiments, however, despite biochemical constraint about the size of ribosome-protected fragments, the outcome of such analysis is heavily influenced by the experimental protocol used.
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83 More read lengths can be chosen, but they have to display a strong frame preference.
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84
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85 From the output, user shall determine the appropriate
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86 read lengths and cutoffs which are required
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87 for running ``ribotaper part 3``, ribosome profiling.
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88
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89 ]]></help>
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90 <citations>
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91 <citation type="doi">10.1038/nmeth.3688</citation>
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92 </citations>
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93 </tool>