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annotate flaimapper.xml @ 2:affc5ec4f65a draft

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author yhoogstrate
date Fri, 31 Jul 2015 05:07:26 -0400
parents 96d135d3c57f
children efd29213e8e5
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper" name="FlaiMapper" version="1.2.1.w1">
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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="1.2.1">flaimapper</requirement>
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6 </requirements>
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8 <stdio>
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9 <regex match="in parse_gff.*?ValueError: invalid literal for int\(\) with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\n" />
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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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23 #for $alignment in $alignments
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24 $alignment
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25 #end for
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26 </command>
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28 <inputs>
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29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
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31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
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33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
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34
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35 <param name="output_format" type="select" label="Output format">
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36 <option value="1">Tabular (1 fragment per column)</option>
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37 <option value="2">Tabular (1 precursor per column)</option>
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38 <option value="3">GenBank</option>
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39 <!-- option value="gtf">GTF/GFF</option -->
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40 </param>
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41 </inputs>
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42
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43 <outputs>
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44 <data format="tabular" name="output" label="${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>
1
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48 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
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49 <param name="alignments" value="test1/snord81.bam" ftype="bam" />
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50 <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" />
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51 <param name="fasta" value="test1/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="test1/snord81.flaimapper.txt" />
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55 </test>
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56 <test><!-- Testing "Full genome alignment"-type analysis -->
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57 <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" />
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58 <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" />
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59 <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" />
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60 <param name="output_format" value="1" />
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61
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62 <output name="output" file="test2/test_genomic_flaimapper_output.txt" />
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63 </test>
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64 </tests>
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65
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66 <help>
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67 FlaiMapper wrapper for Galaxy
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68 =============================
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69
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70 https://github.com/yhoogstrate/flaimapper
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71 http://www.ncbi.nlm.nih.gov/pubmed/25338717
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72 http://dx.doi.org/10.1093/bioinformatics/btu696
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73
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74 Fragment Location Annotation Identification Mapper
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76 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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77
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79 Input
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80 -----
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81
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82 Alignments
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83 **********
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84
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85 Aligned reads from small RNA-Seq experiments have to be provided in the BAM format.
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86 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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87
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88 Mask File
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89 *********
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90
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91 There are two strategies to analyze using FlaiMapper:
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92
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93 - Relative to mature ncRNA sequences
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94 - Relative to chromosomes
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95
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96 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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97
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98 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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99 - http://www.ensembl.org/info/website/upload/gff.html
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100
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101 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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102
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103
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104 You can access **ncRNAdb09** GTF file at the following URL:
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105 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
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106
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107 Fasta sequence
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108 **************
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109
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110 The reference sequence should be provided in FASTA format.
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111
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112 You can access **ncRNAdb09** FASTA file at the following URL:
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113 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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114
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115 Example- and reference data
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116 ***************************
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117
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118 To align reads to ncRNA you need aligner specific indexed version of the reference. We have made
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119 the following available for ncRNAdb09:
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120
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121 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
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122 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
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123
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124 If you want to test FlaiMapper with example data you can obtain several
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125 alignment files from the following directory tree:
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126
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127 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
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128
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129 Installation
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130 ------------
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131
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132 The wrapper makes use of easy_install to install a python egg. Please
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133 ensure you have easy_install installed.
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134
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135 License
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136 -------
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137
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138 **flaimapper** and **wrapper**:
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139
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140 GPL (>=3)
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141
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142 **pysam**:
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143
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144 The MIT License
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145
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146 Contact
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147 -------
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148
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149 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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150 Medical Center (Rotterdam, Netherlands).
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151
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152
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153 Development
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154 -----------
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155
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156 * Repository-Maintainer: Youri Hoogstrate
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157 * Repository-Developers: Youri Hoogstrate
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158
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159 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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160
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161 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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162 Medical Center (Rotterdam, Netherlands).
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163
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164 </help>
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165
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166 <citations>
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167 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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168 </citations>
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169 </tool>