Mercurial > repos > rnateam > ribotaper

annotate ribotaper_part1_create_annotation_files.xml @ 0:bade631353d2 draft

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author rnateam
date Wed, 30 Nov 2016 16:44:53 -0500
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bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.3.1a">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_annotations_files.bash
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11 "$gtf"
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12 "$fa"
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13 "$ccdsid"
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14 "$appris"
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15 "annotation_path"
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16 &&
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17 tar
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18 "czvf"
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19 "$output2"
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20 "annotation_path"
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21
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22 ]]></command>
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23 <inputs>
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24 <param name="gtf" type="data" format="GTF" label="GTF"
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25 help="GTF should contain:
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26 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row.
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27 "/>
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28 <param name="fa" type="data" format="fasta" label="Genome fasta file" help="FASTA-format, indexed and not repeat masked."/>
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29 <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use ccdsid? (valid for Human Gencode 19 and Mouse Gencode M3 )"
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30 help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS.
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31 "/>
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32 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )"
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33 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a gene does not have appris transcript, all the annotated transcript structures are used.
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34 "/>
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35 </inputs>
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36 <outputs>
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37 <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
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38 <data name="output2" format="tar" label="annotation_path"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="gtf" value="test.gtf"/>
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43 <param name="fa" value="test.fa"/>
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44 <param name="ccdsid" value="true"/>
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45 <param name="appris" value="true"/>
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46 <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 Overview
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51 --------
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52
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53 RiboTaper is an analysis pipeline for Ribosome Profiling
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54 (Ribo-seq) experiments,
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55 which exploits the triplet periodicity of
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56 ribosomal footprints to call translated regions.
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57 See
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58 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
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59
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60
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61 The Ribotaper Galaxy tool set consists of three tools:
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62
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63 - ``ribotaper part 1``: creation of annotation files
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64 - ``ribotaper part 2``: metagene analysis for P-sites definition
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65 - ``ribotaper part 3``: ribosome profiling
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66
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67 The order of execution should follow:
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68 ``ribotaper part 1, part 2 and part 3``.
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69
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70 The current tool is ``ribotaper part 1``,
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71 creation of annotation files.
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72
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73 Output
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74 ------
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75
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76 ``Ribotaper part 1`` builds a list of exon coordinates,
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77 exon sequences and transcript structures.
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78
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79 ``Ribotaper part 1`` generates two files:
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80
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81 - **start_stops_FAR** in BED format
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82 - **annotation_path** in format of tar
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83
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84 *Start_stops_FAR*
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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85 is used as an input for ``ribotaper part 2``.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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86 *Annotation_path*
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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87 is used as an input for ``ribotaper part 3``.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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88
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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89
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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90 ]]></help>
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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91 <citations>
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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92 <citation type="doi">10.1038/nmeth.3688</citation>
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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93 </citations>
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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94 </tool>