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comparison flaimapper-gtf-from-fasta.xml @ 0:d6abffbc9ee7 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
author yhoogstrate
date Thu, 21 May 2015 07:26:46 -0400
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.1.5.b">
3 <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
4 <requirements>
5 <requirement type="package" version="0.8.2.1">pysam</requirement>
6 <requirement type="package" version="1.1.5">flaimapper</requirement>
7 </requirements>
8
9 <stdio>
10 <regex
11 match="[fai_load] build FASTA index."
12 source="stderr"
13 level="log"
14 description="The FASTA file is being indexed." />
15 </stdio>
16
17 <version_command>flaimapper --version</version_command>
18
19 <command>
20 gtf-from-fasta
21 -o $output
22 $fasta
23 </command>
24
25 <inputs>
26 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
27 </inputs>
28
29 <outputs>
30 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="fasta" value="ncrnadb09.fa" ftype="fasta" />
36
37 <output name="output" file="ncrnadb09.gtf" />
38 </test>
39 </tests>
40
41 <help>
42 FlaiMapper wrapper for Galaxy
43 =============================
44
45 https://github.com/yhoogstrate/flaimapper
46 http://www.ncbi.nlm.nih.gov/pubmed/25338717
47 http://dx.doi.org/10.1093/bioinformatics/btu696
48
49 Fragment Location Annotation Identification Mapper
50
51 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
52
53 Input formats
54 -------------
55 To make FlaiMapper compatible with both an entire reference genome as a
56 separate ncRNA database, it requires an additional GTF file *(mask file)*.
57 The major difference between an entire reference and a ncRNA database
58 is that an entire reference usually contains multiple ncRNAs per sequence
59 entry (chromosome). While for the ncRNA database, each entry should
60 represent one single mature ncRNA.
61
62 Therefore the mask file that represents to the FASTA file of a ncRNA
63 database will only contain the start- and end positions of each entry.
64 To generate this in an automated fashion, you can make use of this tool
65 *as long as the FASTA file doesn't contain entire chromosomes* but
66 mature ncRNA.
67
68 An example input file is **ncRNAdb09**, available at the following URLs:
69 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
70
71 It should generate a GTF/GFF file (mask file) similar to the following URL:
72 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
73
74 Installation
75 ------------
76
77 The wrapper makes use of easy_install to install a python egg. Please
78 ensure you have easy_install installed.
79
80 License
81 -------
82
83 **flaimapper** and **wrapper**:
84
85 GPL (>=3)
86
87 **pysam**:
88
89 The MIT License
90
91 Contact
92 -------
93
94 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
95 Medical Center (Rotterdam, Netherlands).
96
97
98 Development
99 -----------
100
101 * Repository-Maintainer: Youri Hoogstrate
102 * Repository-Developers: Youri Hoogstrate
103
104 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
105
106 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
107 Medical Center (Rotterdam, Netherlands).
108
109 </help>
110
111 <citations>
112 <citation type="doi">10.1093/bioinformatics/btu696</citation>
113 </citations>
114 </tool>