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comparison ribotaper_part1_create_annotation_files.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_create_annotation" name="ribotaper part 1: creation of annotation files" 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_annotations_files.bash
11 "$gtf"
12 "$fa"
13 "$ccdsid"
14 "$appris"
15 "annotation_path"
16
17 &&
18
19 tar
20 "czvf"
21 "$output2"
22 "annotation_path"
23
24 ]]></command>
25 <inputs>
26 <param name="gtf" type="data" format="GTF" label="GTF"
27 help="GTF should contain:
28 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row.
29 "/>
30 <param name="fa" type="data" format="fasta" label="Genome fasta file" help="FASTA-format, indexed and not repeat masked."/>
31 <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use ccdsid? (valid for Human Gencode 19 and Mouse Gencode M3 )"
32 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.
33 "/>
34 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )"
35 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.
36 "/>
37 </inputs>
38 <outputs>
39 <data name="output1" type="data" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
40 <data name="output2" type="data" format="compressed_archive" label="annotation_path"/>
41 </outputs>
42 <tests>
43 <test>
44 <param name="gtf" value="test.gtf"/>
45 <param name="fa" value="test.fa"/>
46 <param name="ccdsid" value="true"/>
47 <param name="appris" value="true"/>
48 <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
49 </test>
50 </tests>
51 <help><![CDATA[
52 Overview
53 --------
54
55 RiboTaper is an analysis pipeline for Ribosome Profiling
56 (Ribo-seq) experiments,
57 which exploits the triplet periodicity of
58 ribosomal footprints to call translated regions.
59 See
60 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
61
62
63 The Ribotaper Galaxy tool set consists of three tools:
64
65 - ``ribotaper part 1``: creation of annotation files
66 - ``ribotaper part 2``: metagene analysis for P-sites definition
67 - ``ribotaper part 3``: ribosome profiling
68
69 The order of execution should follow:
70 ``ribotaper part 1, part 2 and part 3``.
71
72 The current tool is ``ribotaper part 1``,
73 creation of annotation files.
74
75 Output
76 ------
77
78 ``Ribotaper part 1`` builds a list of exon coordinates,
79 exon sequences and transcript structures.
80
81 ``Ribotaper part 1`` generates two files:
82
83 - **start_stops_FAR** in BED format
84 - **annotation_path** in format of compressed archive
85
86 *Start_stops_FAR*
87 is used as an input for ``ribotaper part 2``.
88 *Annotation_path*
89 is used as an input for ``ribotaper part 3``.
90 ]]></help>
91 <citations>
92 <citation type="doi">10.1038/nmeth.3688</citation>
93 </citations>
94 </tool>