Mercurial > repos > yhoogstrate > flaimapper

annotate flaimapper.xml @ 40:af0ee8dc5471 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
author erasmus-medical-center
date Wed, 16 Aug 2017 11:07:37 -0400
parents 62d46dd9ac42
children 3cf217373ae2
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="flaimapper" name="FlaiMapper" version="2.5.0-0">
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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="2.5.0">flaimapper</requirement>
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6 </requirements>
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8 <version_command><![CDATA[ flaimapper --version 2>&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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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"
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46 help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
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47 </when>
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49 <when value="2">
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50 <param name="offset5p" type="integer" value="4"
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51 label="Add 5'-offset to exon-type entry in GTF output file"
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52 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset5p" />
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53 <param name="offset3p" type="integer" value="4"
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54 label="Add 3'-offset to exon-type entry in GTF output file"
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55 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
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56 </when>
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57 </conditional>
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59 <param name="parameters" type="data" format="txt,tabular" optional="true"
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60 label="(Optional) Custom parameters file" help="" argument="-p" />
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62 </inputs>
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64 <outputs>
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65 <data format="tabular" name="output"
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66 label="${tool.name} on $on_string">
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67 <change_format>
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68 <when input="output_select.output_format" value="1" format="tabular" />
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69 <when input="output_select.output_format" value="2" format="gtf" />
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70 </change_format>
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71 </data>
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72 </outputs>
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74 <tests>
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75 <!-- tabular -->
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76 <!-- Testing "ncRNAdb09 alignment"-type analysis -->
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77 <test>
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78 <param name="alignment" value="snord81.bam" ftype="bam" />
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79 <param name="fasta" value="snord81.fa" ftype="fasta" />
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80 <param name="output_format" value="1" />
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81
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82 <output name="output" file="snord81.flaimapper.txt" />
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83 </test>
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84 <test>
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85 <param name="alignment" value="snord81.bam" ftype="bam" />
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86 <param name="output_format" value="1" />
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87
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88 <output name="output" file="snord81.flaimapper.no-seq.txt" />
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89 </test>
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90 <!-- Testing "Full genome alignment"-type analysis -->
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91 <test>
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92 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
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93 <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
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94 <param name="output_format" value="1" />
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95
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96 <output name="output" file="test_genomic_flaimapper_output.txt" />
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97 </test>
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98 <test>
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99 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
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100 <param name="output_format" value="1" />
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101
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102 <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
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103 </test>
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104
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105 <!-- GTF -->
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106 <!-- Testing "ncRNAdb09 alignment"-type analysis -->
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107 <test>
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108 <param name="alignment" value="snord81.bam" ftype="bam" />
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109 <param name="output_format" value="2" />
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110
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111 <output name="output" file="snord81.flaimapper.gtf" />
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112 </test>
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113 <!-- Testing "Full genome alignment"-type analysis -->
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114 <test>
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115 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
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116 <param name="output_format" value="2" />
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117
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118 <output name="output" file="test_genomic_flaimapper_output.gtf" />
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119 </test>
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120
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121 <!-- test custom parameters -->
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122 <test>
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123 <param name="alignment" value="snord81.bam" ftype="bam" />
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124 <param name="output_format" value="2" />
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125 <param name="offset5p" value="5" />
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126 <param name="offset3p" value="5" />
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127
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128 <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
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129 </test>
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130 <test>
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131 <param name="alignment" value="snord81.bam" ftype="bam" />
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132 <param name="output_format" value="2" />
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133 <param name="parameters" value="filter-parameters.duck.15.txt"/>
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134
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135 <output name="output" file="snord81.flaimapper.duck-15.gtf" />
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136 </test>
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137 </tests>
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138
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139 <help><![CDATA[
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140 FlaiMapper wrapper for Galaxy
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141 =============================
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142
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143 Fragment Location Annotation Identification Mapper
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144
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145 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
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146
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147
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148 Input
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149 -----
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150
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151 Alignment
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152 *********
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153
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154 This file has to contain aligned single end reads from a small RNA-Seq experiment, provided in the BAM format.
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155
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156 Prior to running FlaiMapper, it is common to align sequencing reads to either:
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157
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158 - mature ncRNA sequences
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159 - all chromosomes
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160
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161 Example- and reference data
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162 ***************************
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163
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ac69be28e786 FlaiMapper: added wrapper for FASTA-&gt;GTF conversion
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164 The reference sequence should be provided in FASTA format.
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165
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166 You can access **ncRNAdb09** FASTA file at the following URL:
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167 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
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168
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169 If you want to test FlaiMapper with example data you can obtain several
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170 alignment files from the following directory tree:
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171
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172 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
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173
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174 More details are given in the manual at the following website:
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175
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176 https://github.com/yhoogstrate/flaimapper
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177 ]]></help>
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178
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179 <citations>
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180 <citation type="doi">10.1093/bioinformatics/btu696</citation>
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181 </citations>
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182 </tool>