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annotate flaimapper-gtf-from-fasta.xml @ 2:affc5ec4f65a draft

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author yhoogstrate
date Fri, 31 Jul 2015 05:07:26 -0400
parents 96d135d3c57f
children 8faba9df2791
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1">
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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="1.2.1">flaimapper</requirement>
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6 </requirements>
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8 <stdio>
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9 <regex
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10 match="[fai_load] build FASTA index."
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11 source="stderr"
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12 level="log"
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13 description="The FASTA file is being indexed." />
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14 </stdio>
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16 <version_command>flaimapper --version</version_command>
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18 <command>
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19 gtf-from-fasta
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20 -o $output
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21 $fasta
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22 </command>
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23
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24 <inputs>
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25 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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26 </inputs>
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28 <outputs>
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29 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
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30 </outputs>
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32 <tests>
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33 <test>
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34 <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
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35
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36 <output name="output" file="test3/reference.gtf" />
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37 </test>
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38 </tests>
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40 <help>
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41 FlaiMapper wrapper for Galaxy
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42 =============================
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43
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44 https://github.com/yhoogstrate/flaimapper
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45 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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46 http://dx.doi.org/10.1093/bioinformatics/btu696
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47
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48 Fragment Location Annotation Identification Mapper
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49
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50 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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51
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52 Input formats
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53 -------------
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54 To make FlaiMapper compatible with both an entire reference genome as a
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55 separate ncRNA database, it requires an additional GTF file *(mask file)*.
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56 The major difference between an entire reference and a ncRNA database
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57 is that an entire reference usually contains multiple ncRNAs per sequence
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58 entry (chromosome). While for the ncRNA database, each entry should
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59 represent one single mature ncRNA.
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60
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61 Therefore the mask file that represents to the FASTA file of a ncRNA
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62 database will only contain the start- and end positions of each entry.
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63 To generate this in an automated fashion, you can make use of this tool
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64 *as long as the FASTA file doesn't contain entire chromosomes* but
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65 mature ncRNA.
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66
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67 An example input file is **ncRNAdb09**, available at the following URLs:
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68 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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69
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70 It should generate a GTF/GFF file (mask file) similar to the following URL:
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71 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
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72
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73 Installation
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74 ------------
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75
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76 The wrapper makes use of easy_install to install a python egg. Please
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77 ensure you have easy_install installed.
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78
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79 License
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80 -------
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81
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82 **flaimapper** and **wrapper**:
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83
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84 GPL (>=3)
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85
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86 **pysam**:
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87
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88 The MIT License
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89
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90 Contact
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91 -------
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92
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93 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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94 Medical Center (Rotterdam, Netherlands).
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95
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96
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97 Development
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98 -----------
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99
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100 * Repository-Maintainer: Youri Hoogstrate
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101 * Repository-Developers: Youri Hoogstrate
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102
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103 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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104
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105 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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106 Medical Center (Rotterdam, Netherlands).
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107
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108 </help>
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109
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110 <citations>
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111 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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112 </citations>
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113 </tool>