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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper" name="FlaiMapper" version="1.1.2.c">
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3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
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4 <requirements>
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5 <requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
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6 <requirement type="package" version="1.1.2">flaimapper</requirement>
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7 </requirements>
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8
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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 flaimapper
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13 -v
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14 -f $output_format
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15 -o $output
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16 -m $mask
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17 -r $fasta
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18
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19 #for $alignment in $alignments
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20 $alignment
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21 #end for
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22 </command>
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23
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24 <inputs>
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25 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
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26
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27 <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
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28
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29 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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30
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31 <param name="output_format" type="select" label="Output format">
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32 <option value="1">Tabular (1 fragment per column)</option>
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33 <option value="2">Tabular (1 precursor per column)</option>
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34 <option value="3">GenBank</option>
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35 <!-- option value="gtf">GTF/GFF</option -->
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36 </param>
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37 </inputs>
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38
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39 <outputs>
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40 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
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41 </outputs>
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42
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43 <help>
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44 FlaiMapper wrapper for Galaxy
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45 =============================
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46
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47 https://github.com/yhoogstrate/flaimapper
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48 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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49 http://dx.doi.org/10.1093/bioinformatics/btu696
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50
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51 Fragment Location Annotation Identification Mapper
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52
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53 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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54
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55 Input formats
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56 -------------
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57 Alignments should be provided in BAM format.
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58 Gene (MASK) regions should be provided in the GFF/GTF format:
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59
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60 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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61 - http://www.ensembl.org/info/website/upload/gff.html
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62
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63 The reference sequence should be provided in FASTSA format.
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64
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65 Installation
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66 ------------
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67
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68 The wrapper makes use of easy_install to install a python egg. Please
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69 ensure you have easy_install installed.
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70
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71 License
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72 -------
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73
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74 **flaimapper** and **wrapper**:
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75
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76 GPL (>=3)
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77
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78 **pysam**:
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79
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80 The MIT License (>=3)
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81
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82 Contact
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83 -------
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84
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85 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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86 Medical Center (Rotterdam, Netherlands).
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87
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88
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89 Development
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90 -----------
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91
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92 * Repository-Maintainer: Youri Hoogstrate
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93 * Repository-Developers: Youri Hoogstrate
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94
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95 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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96
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97 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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98 Medical Center (Rotterdam, Netherlands).
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99
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100 References
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101 ----------
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102 **FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.**
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103
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104 *Hoogstrat* - Bioinformatics. 2014 Apr 1;30(7):923-30.
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105
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106 *Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673
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107
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108 - http://www.ncbi.nlm.nih.gov/pubmed/25338717
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109 - http://dx.doi.org/10.1093/bioinformatics/btu696
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110 </help>
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111
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112 <citations>
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113 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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114 </citations>
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115 </tool> |
