Mercurial > repos > rnateam > ribotaper

annotate ribotaper_part3_main.xml @ 1:56ffbec351b3 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"
author rnateam
date Tue, 07 Jun 2022 09:22:45 +0000
parents bade631353d2
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1 <tool id="ribotaper_ribosome_profiling" name="ribotaper part 3: ribosome profiling" 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'/>
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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 #if $annotation_path.is_of_type("tgz")
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12 tar -xzvf '${annotation_path}' &&
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13 #else
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14 tar -xvf '${annotation_path}' &&
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15 #end if
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16 Ribotaper.sh
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17 '${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 ]]></command>
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24 <inputs>
1
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25 <param name="annotation_path" type="data" format="tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
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26 <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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27 <param name="rna_bam" type="data" format="BAM" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
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28 <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.
1
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29 Please run 'ribotaper part 2' to deterimine appropriate values.">
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30 <sanitizer invalid_char="">
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31 <valid initial="string.digits">
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32 <add value="," />
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33 </valid>
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34 </sanitizer>
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35 <validator type="regex">[0-9,]+</validator>
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36 </param>
0
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37 <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.
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38 Please run 'ribotaper part 2' to deterimine appropriate values.">
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39 <sanitizer invalid_char="">
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40 <valid initial="string.digits">
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41 <add value="," />
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42 </valid>
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43 </sanitizer>
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44 <validator type="regex">[0-9,]+</validator>
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45 </param>
0
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46 </inputs>
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47 <outputs>
1
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48 <data name="output1" format="pdf" from_work_dir="quality_check_plots.pdf" label="${tool.name} on ${on_string}: QC plots"/>
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49 <data name="output2" format="tabular" from_work_dir="ORFs_genes_found" label="${tool.name} on ${on_string}: Summary of translated ORFs"/>
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50 <data name="output3" format="tabular" from_work_dir="ORFs_max" label="${tool.name} on ${on_string}: Translated ORFs (max)"/>
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51 <data name="output4" format="tabular" from_work_dir="ORFs_max_filt" label="${tool.name} on ${on_string}: Translated ORFs (max_filt)"/>
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52 <data name="output5" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="${tool.name} on ${on_string}: Translated ORFs (sorted)"/>
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53 <data name="output6" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="${tool.name} on ${on_string}: Translated ORFs (filtered/sorted)"/>
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54 <data name="output7" format="fasta" from_work_dir="protein_db_max.fasta" label="${tool.name} on ${on_string}: Protein DB"/>
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55 <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="${tool.name} on ${on_string}: ORF categories (length/coverage)"/>
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56 </outputs>
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57 <tests>
1
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58 <test expect_num_outputs="8">
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59 <param name="annotation_path" value="annotation_path.tgz"/>
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60 <param name="ribo_bam" value="test_ribo.bam"/>
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61 <param name="rna_bam" value="test_rna.bam"/>
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62 <output name="output2" file="ORFs_genes_found"/>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 RiboTaper is an analysis pipeline for Ribosome Profiling
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67 (Ribo-seq) experiments,
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68 which exploits the triplet periodicity of
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69 ribosomal footprints to call translated regions.
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70 See
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71 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
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72
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73
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74 The Ribotaper Galaxy tool set consists of three tools:
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75
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76 - ``ribotaper part 1``: creation of annotation files
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77 - ``ribotaper part 2``: metagene analysis for P-sites definition
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78 - ``ribotaper part 3``: ribosome profiling
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79
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80 The order of execution should follow:
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81 ``ribotaper part 1, part 2 and part 3``.
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82
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83 The current tool is ``ribotaper part 3``,
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84 ribosome profiling.
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85
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86 Outputs
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87 --------
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88
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89 **QC plots**:
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90 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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91 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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92 Very important are also the length/coverage statistics for the Ribo-seq (bottom right):
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93 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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94
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95 **Summary of translated ORFs**:
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96 Tab-separated values for the number of ORFs found and their corresponding genes, for the different ORF categories.
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97
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98 **Translated ORFs (max, max_filt)**:
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99 Tab-separated file containing information about detected ORFs.
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100 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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101
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102 **Protein DB**:
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103 Fasta file of the detected ORFs peptide sequence, suitable as an alternative protein database (not filtered for multimapping)
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104
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105 **Translated ORFs (sorted, filtered/sorted)**:
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106 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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107
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108 **ORF categories (length/coverage)**:
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109 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation.
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110
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111 ]]></help>
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112 <expand macro="citations"/>
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113 </tool>