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comparison ribotaper_part1_create_annotation_files.xml @ 0:bade631353d2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
author rnateam
date Wed, 30 Nov 2016 16:44:53 -0500
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1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="1.3.1a">ribotaper</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8
9 <command><![CDATA[
10 create_annotations_files.bash
11 "$gtf"
12 "$fa"
13 "$ccdsid"
14 "$appris"
15 "annotation_path"
16 &&
17 tar
18 "czvf"
19 "$output2"
20 "annotation_path"
21
22 ]]></command>
23 <inputs>
24 <param name="gtf" type="data" format="GTF" label="GTF"
25 help="GTF should contain:
26 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row.
27 "/>
28 <param name="fa" type="data" format="fasta" label="Genome fasta file" help="FASTA-format, indexed and not repeat masked."/>
29 <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use ccdsid? (valid for Human Gencode 19 and Mouse Gencode M3 )"
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.
31 "/>
32 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )"
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.
34 "/>
35 </inputs>
36 <outputs>
37 <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
38 <data name="output2" format="tar" label="annotation_path"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="gtf" value="test.gtf"/>
43 <param name="fa" value="test.fa"/>
44 <param name="ccdsid" value="true"/>
45 <param name="appris" value="true"/>
46 <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
47 </test>
48 </tests>
49 <help><![CDATA[
50 Overview
51 --------
52
53 RiboTaper is an analysis pipeline for Ribosome Profiling
54 (Ribo-seq) experiments,
55 which exploits the triplet periodicity of
56 ribosomal footprints to call translated regions.
57 See
58 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
59
60
61 The Ribotaper Galaxy tool set consists of three tools:
62
63 - ``ribotaper part 1``: creation of annotation files
64 - ``ribotaper part 2``: metagene analysis for P-sites definition
65 - ``ribotaper part 3``: ribosome profiling
66
67 The order of execution should follow:
68 ``ribotaper part 1, part 2 and part 3``.
69
70 The current tool is ``ribotaper part 1``,
71 creation of annotation files.
72
73 Output
74 ------
75
76 ``Ribotaper part 1`` builds a list of exon coordinates,
77 exon sequences and transcript structures.
78
79 ``Ribotaper part 1`` generates two files:
80
81 - **start_stops_FAR** in BED format
82 - **annotation_path** in format of tar
83
84 *Start_stops_FAR*
85 is used as an input for ``ribotaper part 2``.
86 *Annotation_path*
87 is used as an input for ``ribotaper part 3``.
88
89
90 ]]></help>
91 <citations>
92 <citation type="doi">10.1038/nmeth.3688</citation>
93 </citations>
94 </tool>