Mercurial > repos > yhoogstrate > flaimapper

annotate flaimapper.xml @ 38:ee6d8c07205b draft

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author yhoogstrate
date Mon, 23 Jan 2017 03:08:41 -0500
parents 3074e91f9f80
children 62d46dd9ac42
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper" name="FlaiMapper" version="2.3.4-0">
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3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
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4 <requirements>
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5 <requirement type="package" version="2.3.4">flaimapper</requirement>
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6 </requirements>
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7
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8 <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 flaimapper
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12 -v
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13 -f '${output_select.output_format}'
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14 -o '${output}'
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16 #if $output_select.output_format == '1':
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17 #if $output_select.fasta:
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18 -r '${output_select.fasta}'
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19 #end if
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20 #else
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21 --offset5p ${output_select.offset5p}
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22 --offset3p ${output_select.offset3p}
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23 #end if
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25 #if $parameters:
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26 -p '${parameters}'
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27 #end if
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29 '${alignment}'
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30 ]]></command>
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32 <inputs>
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33 <param name="alignment" type="data" format="bam" multiple="false"
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34 label="Alignment file"
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35 help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />
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36
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37 <conditional name="output_select">
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38 <param name="output_format" type="select" label="Output format" argument="-f">
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39 <option value="1">Tabular</option>
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40 <option value="2">GTF</option>
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41 </param>
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43 <when value="1">
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44 <param name="fasta" type="data" format="fasta" optional="true"
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45 label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database" help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
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46 </when>
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47
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48 <when value="2">
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49 <param name="offset5p" type="integer" value="4"
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50 label="5' offset added to the exon-type GTF entry"
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51 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset5p" />
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52 <param name="offset3p" type="integer" value="4"
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53 label="3' offset added to the exon-type GTF entry"
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54 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset3p" />
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55 </when>
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56 </conditional>
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58 <param name="parameters" type="data" format="txt,tabular" optional="true"
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59 label="(Optional) Custom parameters file" help="" argument="-p" />
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60
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61 </inputs>
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62
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63 <outputs>
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64 <data format="tabular" name="output"
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65 label="${tool.name} on $on_string">
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66 <change_format>
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67 <when input="output_select.output_format" value="1" format="tabular" />
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68 <when input="output_select.output_format" value="2" format="gtf" />
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69 </change_format>
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70 </data>
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71 </outputs>
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72
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73 <tests>
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74 <!-- tabular -->
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75 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
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76 <param name="alignment" value="snord81.bam" ftype="bam" />
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77 <param name="fasta" value="snord81.fa" ftype="fasta" />
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78 <param name="output_format" value="1" />
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79
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80 <output name="output" file="snord81.flaimapper.txt" />
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81 </test>
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82 <test>
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83 <param name="alignment" value="snord81.bam" ftype="bam" />
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84 <param name="output_format" value="1" />
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85
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86 <output name="output" file="snord81.flaimapper.no-seq.txt" />
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87 </test>
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88 <test><!-- Testing "Full genome alignment"-type analysis -->
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89 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
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90 <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
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91 <param name="output_format" value="1" />
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92
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93 <output name="output" file="test_genomic_flaimapper_output.txt" />
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94 </test>
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95 <test>
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96 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
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97 <param name="output_format" value="1" />
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98
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99 <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
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100 </test>
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101
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102 <!-- GTF -->
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103 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
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104 <param name="alignment" value="snord81.bam" ftype="bam" />
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105 <param name="output_format" value="2" />
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106
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107 <output name="output" file="snord81.flaimapper.gtf" />
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108 </test>
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109 <test><!-- Testing "Full genome alignment"-type analysis -->
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110 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
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111 <param name="output_format" value="2" />
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112
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113 <output name="output" file="test_genomic_flaimapper_output.gtf" />
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114 </test>
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115
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116 <!-- test custom parameters -->
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117 <test>
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118 <param name="alignment" value="snord81.bam" ftype="bam" />
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119 <param name="output_format" value="2" />
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120 <param name="offset5p" value="5" />
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121 <param name="offset3p" value="5" />
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122
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123 <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
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124 </test>
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125 <test>
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126 <param name="alignment" value="snord81.bam" ftype="bam" />
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127 <param name="output_format" value="2" />
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128 <param name="parameters" value="filter-parameters.duck.15.txt"/>
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129
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130 <output name="output" file="snord81.flaimapper.duck-15.gtf" />
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131 </test>
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132 </tests>
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133
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134 <help><![CDATA[
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135 FlaiMapper wrapper for Galaxy
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136 =============================
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137
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138 Fragment Location Annotation Identification Mapper
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139
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140 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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141
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142
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143 Input
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144 -----
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145
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146 Alignment
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147 *********
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148
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149 This file has to contain aligned single end reads from a small RNA-Seq experiment, provided in the BAM format.
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150
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151 Prior to running FlaiMapper, it is common to align sequencing reads to either:
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152
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153 - mature ncRNA sequences
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154 - all chromosomes
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155
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156 Example- and reference data
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157 ***************************
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158
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159 The reference sequence should be provided in FASTA format.
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160
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161 You can access **ncRNAdb09** FASTA file at the following URL:
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162 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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163
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164 If you want to test FlaiMapper with example data you can obtain several
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165 alignment files from the following directory tree:
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166
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167 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
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168
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169 More details are given in the manual at the following website:
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170
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171 https://github.com/yhoogstrate/flaimapper
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172 ]]></help>
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173
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174 <citations>
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175 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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176 </citations>
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177 </tool>