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comparison ribotaper_part3_main.xml @ 0:93b90466d533 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit a3232e388d52097083f2662ccb26351fdc2f2412-dirty
author rnateam
date Tue, 07 Jun 2016 17:49:46 -0400
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1 <tool id="ribotaper_ribosome_profiling" name="ribotaper part 3: ribosome profiling" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="1.3.1">ribotaper</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8
9 <command><![CDATA[
10 tar
11 "xzvf"
12 "$annotation_path"
13
14 &&
15
16 Ribotaper.sh
17 "$ribo_bam"
18 "$rna_bam"
19 "annotation_path"
20 "$read_lenghts_ribo1,$read_lenghts_ribo2,$read_lenghts_ribo3"
21 "$cutoff1,$cutoff2,$cutoff3"
22 "\${GALAXY_SLOTS:-12}"
23
24 ]]></command>
25 <inputs>
26 <param name="annotation_path" type="data" format="compressed_archive" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
27 <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
28 <param name="rna_bam" type="data" format="BAM" label="rna_bam" help="RNA-seq alignment file in BAM format."/>
29 <param name="read_lenghts_ribo1" type="text" value="26" label="Read length 1" help="Read length 1, which is used for P-site calculation. Default is '26' but it varies a lot in different datasets. Please run 'ribotaper part 2' to deterimine a appropriate value."/>
30 <param name="read_lenghts_ribo2" type="text" value="28" label="Read length 2" help="Read length 2, which is used for P-site calculation. Default is '28' but it varies a lot in different datasets. Please run 'ribotaper part 2' to deterimine a appropriate value"/>
31 <param name="read_lenghts_ribo3" type="text" value="29" label="Read length 3" help="Read length 3, which is used for P-site calculation. Default is '29' but it varies a lot in different datasets. Please run 'ribotaper part 2' to deterimine a appropriate value"/>
32 <param name="cutoff1" type="text" value="9" label="Cutoff 1" help="Offset 1, which is used for P-sites calculation. Default is '9' but it varies a lot in different datasets.
33 Please run 'ribotaper part 2' to deterimine a appropriate value."/>
34 <param name="cutoff2" type="text" value="12" label="Cutoff 2" help="Offset 2, which is used for P-sites calculation. Default is '12' but it varies a lot in different datasets.
35 Please run 'ribotaper part 2' to deterimine a appropriate value."/>
36 <param name="cutoff3" type="text" value="12" label="Cutoff 3" help="Offset 3, which is used for P-sites calculation. Default is '12' but it varies a lot in different datasets.
37 Please run 'ribotaper part 2' to deterimine a appropriate value."/>
38 </inputs>
39 <outputs>
40 <data name="output1" type="data" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
41 <data name="output2" type="data" format="tabular" from_work_dir="ORFs_genes_found" label="Summary of translated ORFs"/>
42 <data name="output3" type="data" format="tabular" from_work_dir="ORFs_max" label="Translated ORFs (max)"/>
43 <data name="output4" type="data" format="tabular" from_work_dir="ORFs_max_filt" label="Translated ORFs (max_filt)"/>
44 <data name="output5" type="data" format="bed" from_work_dir="translated_ORFs_sorted.bed" label="Translated ORFs (sorted)"/>
45 <data name="output6" type="data" format="bed" from_work_dir="translated_ORFs_filtered_sorted.bed" label="Translated ORFs (filtered/sorted)"/>
46 <data name="output7" type="data" format="fasta" from_work_dir="protein_db_max.fasta" label="Protein DB"/>
47 <data name="output8" type="data" format="pdf" from_work_dir="Final_ORF_results.pdf" label="ORF categories (length/coverage)"/>
48 </outputs>
49 <tests>
50 <test>
51 <param name="annotation_path" value="annotation_path.tgz" ftype="compressed_archive"/>
52 <param name="ribo_bam" value="test_ribo.bam"/>
53 <param name="rna_bam" value="test_rna.bam"/>
54 <param name="read_lenghts_ribo1" value="26"/>
55 <param name="read_lenghts_ribo2" value="28"/>
56 <param name="read_lenghts_ribo3" value="29"/>
57 <param name="cutoff1" value="9"/>
58 <param name="cutoff2" value="12"/>
59 <param name="cutoff3" value="12"/>
60 <output name="output2" file="ORFs_genes_found"/>
61 </test>
62 </tests>
63 <help><![CDATA[
64 RiboTaper is an analysis pipeline for Ribosome Profiling
65 (Ribo-seq) experiments,
66 which exploits the triplet periodicity of
67 ribosomal footprints to call translated regions.
68 See
69 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
70
71
72 The Ribotaper Galaxy tool set consists of three tools:
73
74 - ``ribotaper part 1``: creation of annotation files
75 - ``ribotaper part 2``: metagene analysis for P-sites definition
76 - ``ribotaper part 3``: ribosome profiling
77
78 The order of execution should follow:
79 ``ribotaper part 1, part 2 and part 3``.
80
81 The current tool is ``ribotaper part 3``,
82 ribosome profiling.
83
84 Outputs
85 --------
86
87 **QC plots**:
88 This plot provides the user statistics about the Ribo-seq and RNA seq data used, together with the assessment of the P-sites calculations.
89 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%.
90 Very important are also the length/coverage statistics for the Ribo-seq (bottom right):
91 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.
92
93 **Summary of translated ORFs**:
94 Tab-separated values for the number of ORFs found and their corresponding genes, for the different ORF categories.
95
96 **Translated ORFs (max, max_filt)**:
97 Tab-separated file containing information about detected ORFs.
98 Translated ORFs (max_filt) contains ORFs filtered for excessive multimapping and ORFs in non-coding genes overlapping known coding regions (recommended for further analysis).
99
100 **Protein DB**:
101 Fasta file of the detected ORFs peptide sequence, suitable as an alternative protein database (not filtered for multimapping)
102
103 **Translated ORFs (sorted, filtered/sorted)**:
104 BED files with genomic coordinates for the detected ORFs. The total number of P-sites along the ORF is reported on the 5th column.
105
106 **ORF categories (length/coverage)**:
107 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation.
108
109 Important notes
110 ----------------
111
112 - We ran the RiboTaper analysis on an SGE cluster, using 7 cores and h_vmem 8G. For each dataset, the complete RiboTaper workflow (from the bam files to final results) took ~ 1 day.
113
114 - The current RiboTaper framework is not designed to identify and quantify ORFs on different transcripts. This means the transcript annotation is crucial.
115
116 - Be careful about using scaffolds, both in the genome and GTF files, which may slow the whole pipeline.
117
118 ]]></help>
119 <citations>
120 <citation type="doi">10.1038/nmeth.3688</citation>
121 </citations>
122 </tool>