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annotate flaimapper-gtf-from-fasta.xml @ 24:bd695d4cb7c4 draft

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author yhoogstrate
date Sun, 29 Mar 2015 02:43:11 -0400
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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="1.1.5.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 $fasta
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15 </command>
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17 <stdio>
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18 <regex
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19 match="[fai_load] build FASTA index."
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20 source="stderr"
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21 level="log"
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22 description="The FASTA file is being indexed." />
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23 </stdio>
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24
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25 <inputs>
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26 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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27 </inputs>
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28
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29 <outputs>
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30 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
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31 </outputs>
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33 <tests>
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34 <test>
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35 <param name="fasta" value="ncrnadb09.fa" />
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36
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37 <param name="output" value="ncrnadb09.gtf" />
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38 </test>
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39 </tests>
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40
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41 <help>
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42 FlaiMapper wrapper for Galaxy
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43 =============================
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44
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45 https://github.com/yhoogstrate/flaimapper
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46 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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47 http://dx.doi.org/10.1093/bioinformatics/btu696
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48
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49 Fragment Location Annotation Identification Mapper
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50
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51 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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52
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53 Input formats
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54 -------------
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55 To make FlaiMapper compatible with both an entire reference genome as a
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56 separate ncRNA database, it requires an additional GTF file *(mask file)*.
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57 The major difference between an entire reference and a ncRNA database
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58 is that an entire reference usually contains multiple ncRNAs per sequence
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59 entry (chromosome). While for the ncRNA database, each entry should
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60 represent one single mature ncRNA.
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61
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62 Therefore the mask file that represents to the FASTA file of a ncRNA
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63 database will only contain the start- and end positions of each entry.
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64 To generate this in an automated fashion, you can make use of this tool
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65 *as long as the FASTA file doesn't contain entire chromosomes* but
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66 mature ncRNA.
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67
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68 An example input file is **ncRNAdb09**, available at the following URLs:
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69 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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70
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71 It should generate a GTF/GFF file (mask file) similar to the following URL:
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72 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
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73
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74 Installation
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75 ------------
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76
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77 The wrapper makes use of easy_install to install a python egg. Please
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78 ensure you have easy_install installed.
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79
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80 License
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81 -------
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82
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83 **flaimapper** and **wrapper**:
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84
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85 GPL (>=3)
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86
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87 **pysam**:
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88
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89 The MIT License
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90
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91 Contact
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92 -------
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93
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94 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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95 Medical Center (Rotterdam, Netherlands).
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96
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97
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98 Development
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99 -----------
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100
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101 * Repository-Maintainer: Youri Hoogstrate
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102 * Repository-Developers: Youri Hoogstrate
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103
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104 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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105
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106 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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107 Medical Center (Rotterdam, Netherlands).
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108
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109 </help>
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110
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111 <citations>
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112 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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113 </citations>
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114 </tool>