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annotate flaimapper-gtf-from-fasta.xml @ 20:ac69be28e786 draft

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FlaiMapper: added wrapper for FASTA->GTF conversion
author yhoogstrate
date Wed, 25 Mar 2015 12:37:45 -0400
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children 262d9457ad84
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper" name="FlaiMapper" version="1.1.5.b">
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3 <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
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4 <requirements>
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5 <requirement type="package" version="0.8.2.1">pysam</requirement>
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6 <requirement type="package" version="1.1.5">flaimapper</requirement>
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7 </requirements>
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8
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9 <version_command>flaimapper --version</version_command>
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10
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11 <command>
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12 gtf-from-fasta
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13 -o $output
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14 $fasta
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15 </command>
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16
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17 <inputs>
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18 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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19 </inputs>
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20
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21 <outputs>
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22 <data format="gtf" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
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23 </outputs>
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24
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25 <help>
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26 FlaiMapper wrapper for Galaxy
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27 =============================
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28
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29 https://github.com/yhoogstrate/flaimapper
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30 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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31 http://dx.doi.org/10.1093/bioinformatics/btu696
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32
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33 Fragment Location Annotation Identification Mapper
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34
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35 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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36
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37 Input formats
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38 -------------
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39 To make FlaiMapper compatible with both an entire reference genome as a
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40 separate ncRNA database, it requires an additional GTF file *(mask file)*.
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41 The major difference between an entire reference and a ncRNA database
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42 is that an entire reference usually contains multiple ncRNAs per sequence
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43 entry (chromosome). While for the ncRNA database, each entry should
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44 represent one single mature ncRNA.
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45
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46 Therefore the mask file that represents to the FASTA file of a ncRNA
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47 database will only contain the start- and end positions of each entry.
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48 To generate this in an automated fashion, you can make use of this tool
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49 *as long as the FASTA file doesn't contain entire chromosomes* but
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50 mature ncRNA.
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51
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52 An example input file is **ncRNAdb09**, available at the following URLs:
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53 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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54
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55 It should generate a GTF/GFF file (mask file) similar to the following URL:
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56 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
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57
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58 Installation
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59 ------------
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60
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61 The wrapper makes use of easy_install to install a python egg. Please
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62 ensure you have easy_install installed.
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63
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64 License
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65 -------
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66
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67 **flaimapper** and **wrapper**:
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68
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69 GPL (>=3)
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70
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71 **pysam**:
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72
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73 The MIT License
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74
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75 Contact
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76 -------
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77
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78 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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79 Medical Center (Rotterdam, Netherlands).
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80
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81
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82 Development
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83 -----------
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84
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85 * Repository-Maintainer: Youri Hoogstrate
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86 * Repository-Developers: Youri Hoogstrate
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87
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88 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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89
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90 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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91 Medical Center (Rotterdam, Netherlands).
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92
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93 </help>
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94
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95 <citations>
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96 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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97 </citations>
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98 </tool>