Mercurial > repos > rnateam > ribotaper

annotate ribotaper_part2_create_metaplots.xml @ 5:9bc0a9b45b8b draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 6ede79703d2f4ed200c5e1d273cad674be486900"
author rnateam
date Wed, 08 Jun 2022 15:05:03 +0000
parents 579b3be2559f
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1 <tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile='20.01'>
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro='bio_tools'/>
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6 <expand macro='requirements'/>
0
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 create_metaplots.bash
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12 "$ribo_bam"
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13 "$start_stops_FAR"
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14 "metagene"
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15 &&
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16 find "metaplots"
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17 "-name"
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18 "metagene*.pdf"
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19 | sort | xargs gs
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20 "-dAutoRotatePages=/None"
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21 "-dBATCH"
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22 "-dNOPAUSE"
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23 "-q"
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24 "-sDEVICE=pdfwrite"
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25 "-sOutputFile=merged_metagene.pdf"
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26 ]]></command>
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27 <inputs>
3
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28 <param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
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29 <param name="start_stops_FAR" type="data" format="bed" label="Start_stops FAR" help="Please run 'ribotaper part 1' to generate the table."/>
0
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30 </inputs>
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31 <outputs>
3
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32 <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (figures)"/>
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33 <data name="output2" format="tabular" from_work_dir="metagene" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (table)"/>
0
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34 </outputs>
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35 <tests>
3
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36 <test expect_num_outputs="2">
0
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37 <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
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38 <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed" ftype="bed"/>
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39 <output name="output2" file="metagene"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 Overview
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44 --------
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45
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46 RiboTaper is an analysis pipeline for Ribosome Profiling
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47 (Ribo-seq) experiments,
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48 which exploits the triplet periodicity of
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49 ribosomal footprints to call translated regions.
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50 See
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51 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
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52
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53
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54 The Ribotaper Galaxy tool set consists of three tools:
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55
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56 - ``ribotaper part 1``: creation of annotation files
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57 - ``ribotaper part 2``: metagene analysis for P-sites definition
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58 - ``ribotaper part 3``: ribosome profiling
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59
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60 The order of execution should follow:
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61 ``ribotaper part 1, part 2 and part 3``.
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62
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63 The current tool is ``ribotaper part 2``,
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64 metagene analysis for P-sites definition.
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65
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66 Output
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67 --------
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68
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69 ``Ribotaper part 2`` generates two files:
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70
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71 - **Metagene analysis results for P-sites definition** in pdf format
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72 - **Metagene analysis results for P-sites definition** in tablular format
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73
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74 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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75 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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76 These plots should help you decide which read lengths to use and with which cutoff.
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77 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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78 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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79 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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80 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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81 More read lengths can be chosen, but they have to display a strong frame preference.
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82
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83 From the output, user shall determine the appropriate
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84 read lengths and cutoffs which are required
93b90466d533 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit a3232e388d52097083f2662ccb26351fdc2f2412-dirty
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85 for running ``ribotaper part 3``, ribosome profiling.
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86
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87 ]]></help>
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88 <expand macro="citations"/>
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89 </tool>