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annotate flaimapper.xml @ 0:d6abffbc9ee7 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
author yhoogstrate
date Thu, 21 May 2015 07:26:46 -0400
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d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
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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.a">
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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>
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6 <requirement type="package" version="1.1.5">flaimapper</requirement>
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7 </requirements>
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9 <stdio>
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10 <regex match="[fai_load] build FASTA index." source="stderr" level="log" />
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11 </stdio>
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13 <version_command>flaimapper --version</version_command>
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15 <command>
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16 flaimapper
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17 -v
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18 -f $output_format
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19 -o $output
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20 -m $mask
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21 -r $fasta
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22
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23 #for $alignment in $alignments
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24 $alignment
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25 #end for
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26 </command>
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27
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28 <inputs>
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29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
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30
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31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
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32
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33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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34
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35 <param name="output_format" type="select" label="Output format">
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36 <option value="1">Tabular (1 fragment per column)</option>
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37 <option value="2">Tabular (1 precursor per column)</option>
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38 <option value="3">GenBank</option>
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39 <!-- option value="gtf">GTF/GFF</option -->
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40 </param>
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41 </inputs>
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42
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43 <outputs>
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44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param name="alignments" value="snord81.bam" ftype="bam" />
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50 <param name="mask" value="ncrnadb09.gtf" ftype="gtf" />
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51 <param name="fasta" value="ncrnadb09.fa" ftype="fasta" />
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52 <param name="output_format" value="1" />
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53
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54 <output name="output" file="snord81.flaimapper.txt" />
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55 </test>
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56 </tests>
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57
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58 <help>
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59 FlaiMapper wrapper for Galaxy
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60 =============================
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61
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62 https://github.com/yhoogstrate/flaimapper
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63 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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64 http://dx.doi.org/10.1093/bioinformatics/btu696
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65
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66 Fragment Location Annotation Identification Mapper
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67
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68 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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69
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70
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71 Input
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72 -----
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73
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74 Alignments
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75 **********
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76
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77 Aligned reads from small RNA-Seq experiments have to be provided in the BAM format.
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78 In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments.
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79
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80 Mask File
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81 *********
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82
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83 There are two strategies to analyze using FlaiMapper:
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84
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85 - Relative to mature ncRNA sequences
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86 - Relative to chromosomes
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87
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88 Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (MASK) regions should be provided in the GFF/GTF format:
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89
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90 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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91 - http://www.ensembl.org/info/website/upload/gff.html
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92
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93 If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one.
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94
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95
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96 You can access **ncRNAdb09** GTF file at the following URL:
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97 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
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98
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99 Fasta sequence
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100 **************
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101
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102 The reference sequence should be provided in FASTA format.
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103
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104 You can access **ncRNAdb09** FASTA file at the following URL:
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105 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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106
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107 Example- and reference data
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108 ***************************
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109
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110 To align reads to ncRNA you need aligner specific indexed version of the reference. We have made
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111 the following available for ncRNAdb09:
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112
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113 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
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114 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
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115
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116 If you want to test FlaiMapper with example data you can obtain several
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117 alignment files from the following directory tree:
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118
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119 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
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120
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121 Installation
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122 ------------
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123
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124 The wrapper makes use of easy_install to install a python egg. Please
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125 ensure you have easy_install installed.
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126
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127 License
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128 -------
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129
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130 **flaimapper** and **wrapper**:
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131
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132 GPL (>=3)
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133
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134 **pysam**:
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135
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136 The MIT License
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137
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138 Contact
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139 -------
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140
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141 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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142 Medical Center (Rotterdam, Netherlands).
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143
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144
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145 Development
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146 -----------
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147
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148 * Repository-Maintainer: Youri Hoogstrate
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149 * Repository-Developers: Youri Hoogstrate
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150
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151 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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152
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153 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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154 Medical Center (Rotterdam, Netherlands).
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155
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156 </help>
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157
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158 <citations>
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159 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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160 </citations>
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161 </tool>