Mercurial > repos > rnateam > ribotaper

comparison ribotaper_part2_create_metaplots.xml @ 0:93b90466d533 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children a56343c142d5
comparison
equal deleted inserted replaced
-1:000000000000 0:93b90466d533
1 <tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" 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 create_metaplots.bash
11 "$ribo_bam"
12 "$start_stops_FAR"
13 "metagene"
14
15 &&
16
17 find "metaplots"
18 "-name"
19 "metagene*.pdf"
20 | sort | xargs gs
21 "-dAutoRotatePages=/None"
22 "-dBATCH"
23 "-dNOPAUSE"
24 "-q"
25 "-sDEVICE=pdfwrite"
26 "-sOutputFile=merged_metagene.pdf"
27
28 ]]></command>
29 <inputs>
30 <param name="ribo_bam" type="data" format="bam" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
31 <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/>
32 </inputs>
33 <outputs>
34 <data name="output1" type="data" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
35 <data name="output2" type="data" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
36 </outputs>
37 <tests>
38 <test>
39 <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
40 <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed" ftype="bed"/>
41 <output name="output2" file="metagene"/>
42 </test>
43 </tests>
44 <help><![CDATA[
45 Overview
46 --------
47
48 RiboTaper is an analysis pipeline for Ribosome Profiling
49 (Ribo-seq) experiments,
50 which exploits the triplet periodicity of
51 ribosomal footprints to call translated regions.
52 See
53 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
54
55
56 The Ribotaper Galaxy tool set consists of three tools:
57
58 - ``ribotaper part 1``: creation of annotation files
59 - ``ribotaper part 2``: metagene analysis for P-sites definition
60 - ``ribotaper part 3``: ribosome profiling
61
62 The order of execution should follow:
63 ``ribotaper part 1, part 2 and part 3``.
64
65 The current tool is ``ribotaper part 2``,
66 metagene analysis for P-sites definition.
67
68 Output
69 --------
70
71 ``Ribotaper part 2`` generates two files:
72
73 - **Metagene analysis results for P-sites definition** in pdf format
74 - **Metagene analysis results for P-sites definition** in tablular format
75
76 The outputs include the aggregate profiles around the start and stop codons for the 5'-end of different Ribo-seq read lengths.
77 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.
78 These plots should help you decide which read lengths to use and with which cutoff.
79 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.
80 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.
81 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.
82 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.
83 More read lengths can be chosen, but they have to display a strong frame preference.
84
85 From the output, user shall determine the appropriate
86 read lengths and cutoffs which are required
87 for running ``ribotaper part 3``, ribosome profiling.
88
89 ]]></help>
90 <citations>
91 <citation type="doi">10.1038/nmeth.3688</citation>
92 </citations>
93 </tool>