Mercurial > repos > rnateam > ribotaper

annotate ribotaper_part3_main.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_ribosome_profiling" name="ribotaper part 3: ribosome profiling" 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 tar
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11 "xzvf"
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12 "$annotation_path"
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13
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14 &&
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15
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16 Ribotaper.sh
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17 "$ribo_bam"
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18 "$rna_bam"
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19 "annotation_path"
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20 "$read_lenghts_ribo"
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21 "$cutoff"
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22 "\${GALAXY_SLOTS:-12}"
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23
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24 ]]></command>
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25 <inputs>
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26 <param name="annotation_path" type="data" format="tar" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
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27 <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
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28 <param name="rna_bam" type="data" format="BAM" label="rna_bam" help="RNA-seq alignment file in BAM format."/>
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29 <param name="read_lenghts_ribo" type="text" value="26,28,29" label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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30 Please run 'ribotaper part 2' to deterimine appropriate values."/>
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31 <param name="cutoff" type="text" value="9,12,12" label="Cutoff" help="Cutoffs, comma-separated values, which are used for P-sites calculation. Example, 9,12,12.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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32 Please run 'ribotaper part 2' to deterimine appropriate values."/>
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33 </inputs>
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34 <outputs>
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35 <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
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36 <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/>
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37 <data name="output3" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/>
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38 <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/>
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39 <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/>
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40 <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/>
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41 <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/>
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42 <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="annotation_path" value="annotation_path.tgz" ftype="tar"/>
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47 <param name="ribo_bam" value="test_ribo.bam"/>
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48 <param name="rna_bam" value="test_rna.bam"/>
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49 <output name="output2" file="ORFs_genes_found"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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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 3``,
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71 ribosome profiling.
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72
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73 Outputs
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74 --------
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75
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76 **QC plots**:
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77 This plot provides the user statistics about the Ribo-seq and RNA seq data used, together with the assessment of the P-sites calculations.
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78 Important values are the pie chart showing the agreement between the frame (defined by the P-sites position) and the annotated frame. Reliable P-sites calculations produce an agreement above 90%.
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79 Very important are also the length/coverage statistics for the Ribo-seq (bottom right):
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80 This shows how the P-site calculations can be used to detect active translation in regions of different length and coverage, in a way the user can estimate the precision of the Ribo-seq data, and understand the level or resolution the data allows.
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81
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82 **Summary of translated ORFs**:
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83 Tab-separated values for the number of ORFs found and their corresponding genes, for the different ORF categories.
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84
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85 **Translated ORFs (max, max_filt)**:
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86 Tab-separated file containing information about detected ORFs.
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87 Translated ORFs (max_filt) contains ORFs filtered for excessive multimapping and ORFs in non-coding genes overlapping known coding regions (recommended for further analysis).
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88
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89 **Protein DB**:
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90 Fasta file of the detected ORFs peptide sequence, suitable as an alternative protein database (not filtered for multimapping)
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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91
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92 **Translated ORFs (sorted, filtered/sorted)**:
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93 BED files with genomic coordinates for the detected ORFs. The total number of P-sites along the ORF is reported on the 5th column.
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94
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95 **ORF categories (length/coverage)**:
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96 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation.
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97
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98 ]]></help>
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99 <citations>
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100 <citation type="doi">10.1038/nmeth.3688</citation>
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101 </citations>
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102 </tool>