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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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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" name="FlaiMapper" version="1.1.5.a">
3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</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 match="[fai_load] build FASTA index." source="stderr" level="log" />
11 </stdio>
12
13 <version_command>flaimapper --version</version_command>
14
15 <command>
16 flaimapper
17 -v
18 -f $output_format
19 -o $output
20 -m $mask
21 -r $fasta
22
23 #for $alignment in $alignments
24 $alignment
25 #end for
26 </command>
27
28 <inputs>
29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
30
31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
32
33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
34
35 <param name="output_format" type="select" label="Output format">
36 <option value="1">Tabular (1 fragment per column)</option>
37 <option value="2">Tabular (1 precursor per column)</option>
38 <option value="3">GenBank</option>
39 <!-- option value="gtf">GTF/GFF</option -->
40 </param>
41 </inputs>
42
43 <outputs>
44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
45 </outputs>
46
47 <tests>
48 <test>
49 <param name="alignments" value="snord81.bam" ftype="bam" />
50 <param name="mask" value="ncrnadb09.gtf" ftype="gtf" />
51 <param name="fasta" value="ncrnadb09.fa" ftype="fasta" />
52 <param name="output_format" value="1" />
53
54 <output name="output" file="snord81.flaimapper.txt" />
55 </test>
56 </tests>
57
58 <help>
59 FlaiMapper wrapper for Galaxy
60 =============================
61
62 https://github.com/yhoogstrate/flaimapper
63 http://www.ncbi.nlm.nih.gov/pubmed/25338717
64 http://dx.doi.org/10.1093/bioinformatics/btu696
65
66 Fragment Location Annotation Identification Mapper
67
68 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
69
70
71 Input
72 -----
73
74 Alignments
75 **********
76
77 Aligned reads from small RNA-Seq experiments have to be provided in the BAM format.
78 In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments.
79
80 Mask File
81 *********
82
83 There are two strategies to analyze using FlaiMapper:
84
85 - Relative to mature ncRNA sequences
86 - Relative to chromosomes
87
88 Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (MASK) regions should be provided in the GFF/GTF format:
89
90 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
91 - http://www.ensembl.org/info/website/upload/gff.html
92
93 If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one.
94
95
96 You can access **ncRNAdb09** GTF file at the following URL:
97 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
98
99 Fasta sequence
100 **************
101
102 The reference sequence should be provided in FASTA format.
103
104 You can access **ncRNAdb09** FASTA file at the following URL:
105 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
106
107 Example- and reference data
108 ***************************
109
110 To align reads to ncRNA you need aligner specific indexed version of the reference. We have made
111 the following available for ncRNAdb09:
112
113 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
114 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
115
116 If you want to test FlaiMapper with example data you can obtain several
117 alignment files from the following directory tree:
118
119 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
120
121 Installation
122 ------------
123
124 The wrapper makes use of easy_install to install a python egg. Please
125 ensure you have easy_install installed.
126
127 License
128 -------
129
130 **flaimapper** and **wrapper**:
131
132 GPL (>=3)
133
134 **pysam**:
135
136 The MIT License
137
138 Contact
139 -------
140
141 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
142 Medical Center (Rotterdam, Netherlands).
143
144
145 Development
146 -----------
147
148 * Repository-Maintainer: Youri Hoogstrate
149 * Repository-Developers: Youri Hoogstrate
150
151 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
152
153 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
154 Medical Center (Rotterdam, Netherlands).
155
156 </help>
157
158 <citations>
159 <citation type="doi">10.1093/bioinformatics/btu696</citation>
160 </citations>
161 </tool>