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annotate flaimapper-gtf-from-fasta.xml @ 4:8faba9df2791 draft

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author yhoogstrate
date Fri, 31 Jul 2015 05:30:55 -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="1.2.1.w2">
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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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7
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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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15
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16 <version_command>flaimapper --version</version_command>
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17
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18 <command><![CDATA[
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19 gtf-from-fasta -o $output $fasta
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20 ]]></command>
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21
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22 <inputs>
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23 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="This is the FASTA file that fits the used reference genome (e.g. hg19 or a ncRNA database)." />
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24 </inputs>
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25
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26 <outputs>
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27 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
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28 </outputs>
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29
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30 <tests>
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31 <test>
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32 <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
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33
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34 <output name="output" file="test3/reference.gtf" />
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35 </test>
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36 </tests>
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37
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38 <help><![CDATA[
0
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39 FlaiMapper wrapper for Galaxy
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40 =============================
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42 https://github.com/yhoogstrate/flaimapper
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43 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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44 http://dx.doi.org/10.1093/bioinformatics/btu696
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46 Fragment Location Annotation Identification Mapper
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48 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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50 Input formats
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51 -------------
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52 To make FlaiMapper compatible with both an entire reference genome as a
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53 separate ncRNA database, it requires an additional GTF file *(mask file)*.
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54 The major difference between an entire reference and a ncRNA database
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55 is that an entire reference usually contains multiple ncRNAs per sequence
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56 entry (chromosome). While for the ncRNA database, each entry should
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57 represent one single mature ncRNA.
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58
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59 Therefore the mask file that represents to the FASTA file of a ncRNA
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60 database will only contain the start- and end positions of each entry.
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61 To generate this in an automated fashion, you can make use of this tool
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62 *as long as the FASTA file doesn't contain entire chromosomes* but
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63 mature ncRNA.
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65 An example input file is **ncRNAdb09**, available at the following URLs:
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66 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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67
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68 It should generate a GTF/GFF file (mask file) similar to the following URL:
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69 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
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71 Installation
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72 ------------
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74 The wrapper makes use of easy_install to install a python egg. Please
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75 ensure you have easy_install installed.
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77 License
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78 -------
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80 **flaimapper** and **wrapper**:
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82 GPL (>=3)
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84 **pysam**:
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86 The MIT License
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88 Contact
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89 -------
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91 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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92 Medical Center (Rotterdam, Netherlands).
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95 Development
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96 -----------
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98 * Repository-Maintainer: Youri Hoogstrate
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99 * Repository-Developers: Youri Hoogstrate
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100
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101 * Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
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103 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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104 Medical Center (Rotterdam, Netherlands).
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106 ]]></help>
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107
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108 <citations>
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109 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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110 </citations>
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111 </tool>