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annotate fuma.xml @ 7:77c5a17f335b draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2
author yhoogstrate
date Fri, 09 Oct 2015 10:20:14 -0400
parents b92f986bd0ab
children 9ca5372beeae
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="fuma" name="FuMa" version="2.10.0.a">
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3 <description>match detected fusion genes based on gene names (in particular for RNA-Seq).</description>
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5 <requirements>
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6 <requirement type="package" version="2.7">python</requirement>
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7 <requirement type="package" version="2.10.0">fuma</requirement>
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8 </requirements>
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10 <version_command>fuma --version 2>&amp;1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->
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12 <command><![CDATA[
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13 #import pipes
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15 #set $gene_annotations = []
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16 #set $samples = []
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17 #set $links = []
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19 #for $i, $d in enumerate( $datasets )
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20 #set $sample_name = pipes.quote(str($d['sample'].name))
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22 #set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d['gene_annotation'].file_name) ]
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24 #set $samples = $samples + [ $sample_name + ":" + str($d['format']) + ":" + str($d['sample'].file_name) ]
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25 #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]
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26 #end for
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27
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28 #set $gene_annotations_str = " ".join(gene_annotations)
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29 #set $samples_str = " ".join(samples)
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30 #set $links_str = " ".join(links)
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32 fuma
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33 -m
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34 $params.matching_method
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35
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36 $params.strand_specific_matching
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37 $params.acceptor_donor_order_specific_matchig
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38
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39 -a
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40 $gene_annotations_str
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41 -s
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42 $samples_str
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43 -l
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44 $links_str
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45 #if $params.output_format.value == "list_boolean"
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46 -f list
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47 #else
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48 -f $params.output_format.value
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49 #end if
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50 -o $fuma_overview ;
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52
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53 #if $params.output_format.value == "list_boolean"
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54 fuma-list-to-boolean-list -o tmp.txt $fuma_overview ;
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55 mv tmp.txt $fuma_overview
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56 #end if
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57 ]]></command>
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58
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59 <inputs>
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60 <repeat name="datasets" title="FusionGene Datasets" min="2">
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61 <param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />
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62 <param name="format" type="select" label="Format of dataset">
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63 <option value="chimera">Chimera prettyPrint()</option>
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64 <option value="chimerascan">ChimeraScan</option>
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65 <option value="defuse">DeFuse</option>
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66 <option value="complete-genomics">Complete Genomics var/mastervar</option>
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67 <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>
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68 <option value="fusionmap">FusionMap</option>
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69 <option value="trinity-gmap">GMAP (As step after Trinity)</option>
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70 <option value="oncofuse">OncoFuse</option>
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71 <option value="rna-star_chimeric">STAR (chimeric file)</option>
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72 <option value="star-fusion_final">STAR-Fusion (candidates.final)</option>
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73 <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>
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74 <option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>
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75 <option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>
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76 <option value="tophat-fusion_post_result_html">Tophat Fusion Post (result.html)</option>
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77 </param>
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78 <param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene annotations! Gene annotations should only be different if different reference genome builds were used." />
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79 </repeat>
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80
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81 <conditional name="params">
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82 <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any FuMa parameter.">
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83 <option value="preSet" selected="true">Use Defaults</option>
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84 <option value="full">Full parameter list</option>
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85 </param>
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86 <when value="preSet">
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87 <param name="strand_specific_matching" type="hidden" value="--strand-specific-matching" />
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88 <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--acceptor-donor-order-specific-matching" />
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89 </when>
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90 <when value="full">
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91 <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative.">
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92 <option value="overlap">Overlap</option>
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93 <option value="subset" selected="True">Subset</option>
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94 <option value="egm">Exact Geneset Matching (EGM)</option>
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95 </param>
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96
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97 <param name="strand_specific_matching" type="boolean" checked="True" truevalue="--strand-specific-matching" falsevalue="" label="Consider fusion genes distinct when the breakpoints have different strands" help="Only a limited number of file formats support this feature." />
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98 <param name="acceptor_donor_order_specific_matchig" type="boolean" checked="True" truevalue="--acceptor-donor-order-specific-matching" falsevalue="" label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)" help="This settings is not recommended when fusion genes detected in DNA-Seq are used" />
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99
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100 <param name="output_format" type="select" label="Output format">
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101 <option value="list_boolean" selected="true">List (Boolean)</option>
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102 <option value="list">List</option>
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103 <option value="summary">Count summary</option>
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104 </param>
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105 </when>
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106 </conditional>
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107 </inputs>
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108
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109 <outputs>
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110 <data format="tabular" name="fuma_overview" label="${tool.name} on ${', '.join([ str(d['sample'].hid)+': '+d['sample'].name for d in $datasets ])}" />
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111 </outputs>
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112
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113 <tests>
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114 <test>
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115 <!-- <repeat name="datasets"> -->
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116 <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" />
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117 <param name="datasets_0|format" value="chimerascan" />
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118 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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119 <!-- </repeat> -->
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120 <!-- <repeat name="datasets"> -->
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121 <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" />
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122 <param name="datasets_1|format" value="defuse" />
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123 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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124 <!-- </repeat> -->
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125 <!-- <repeat name="datasets"> -->
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126 <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" />
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127 <param name="datasets_2|format" value="fusionmap" />
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128 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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129 <!-- </repeat> -->
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130 <!-- <repeat name="datasets"> -->
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131 <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" />
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132 <param name="datasets_3|format" value="fusionmap" />
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133 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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134 <!-- </repeat> -->
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135
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136 <param name="settingsType" value="full" />
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137
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138 <param name="matching_method" value="subset" />
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139 <param name="strand_specific_matching" value="--strand-specific-matching" />
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140 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" />
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141 <param name="output_format" value="list_boolean" />
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142
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143 <output name="fuma_overview" file="output_test_1.txt" />
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144 </test>
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145 <test>
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146 <!-- <repeat name="datasets"> -->
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147 <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" />
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148 <param name="datasets_0|format" value="chimerascan" />
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149 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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150 <!-- </repeat> -->
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151 <!-- <repeat name="datasets"> -->
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152 <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" />
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153 <param name="datasets_1|format" value="defuse" />
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154 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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155 <!-- </repeat> -->
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156 <!-- <repeat name="datasets"> -->
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157 <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" />
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158 <param name="datasets_2|format" value="fusionmap" />
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159 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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160 <!-- </repeat> -->
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161 <!-- <repeat name="datasets"> -->
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162 <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" />
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163 <param name="datasets_3|format" value="fusionmap" />
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164 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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165 <!-- </repeat> -->
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166
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167 <param name="settingsType" value="full" />
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168
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169 <param name="matching_method" value="subset" />
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170 <param name="strand_specific_matching" value="" />
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171 <param name="acceptor_donor_order_specific_matchig" value="" />
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172 <param name="output_format" value="list_boolean" />
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173
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174 <output name="fuma_overview" file="output_test_2.txt" />
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175 </test>
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176 </tests>
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177
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178 <help><![CDATA[
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179 ============
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180 Introduction
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181 ============
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182
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183 FuMa (Fusion Matcher) matches predicted fusion events (both genomic and transcriptomic) according to chromosomal location or assocatiated gene annotation(s) where the latter should be genome build inspecific.
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184
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185 Because RNA-Sequencing deals with samples that may have undergrond splicing, reads may split up because of biological processes. If a fusion event takes place, the same thing may happen. Therefore we hypothesize that using spanning read distances may be unreliable, because there are known introns of > 100kb. Therefore, FuMa translates the breakpoint to gene names, and only overlaps breakpoints with the same genename(s).
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186
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187 =====
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188 Usage
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189 =====
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190
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191 After you have uploaded the results of your Fusion Gene detection experiment, and selected the format to be *tabular*, you can start the FuMa wrapper. For each dataset you simply have to add another repeat. Then you have to select a corresponding format:
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192
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193 *******
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194 Formats
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195 *******
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196
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197 +-------------------+-----------------------+-------------------------------------+
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198 |Tools | File | Format string |
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199 +===================+=======================+=====================================+
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200 |Chimera | prettyPrint() output | chimera |
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201 +-------------------+-----------------------+-------------------------------------+
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202 |ChimeraScan | chimeras.bedpe | chimerascan |
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203 +-------------------+-----------------------+-------------------------------------+
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204 |Complete Genomics | highConfidenceJu*.tsv | complete-genomics |
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205 +-------------------+-----------------------+-------------------------------------+
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206 |Complete Genomics | allJunctionsBeta*.tsv | complete-genomics |
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207 +-------------------+-----------------------+-------------------------------------+
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208 |DeFuse | results.txt | defuse |
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209 +-------------------+-----------------------+-------------------------------------+
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210 |DeFuse | results.classify.txt | defuse |
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211 +-------------------+-----------------------+-------------------------------------+
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212 |DeFuse | results.filtered.txt | defuse |
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213 +-------------------+-----------------------+-------------------------------------+
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214 |Fusion Catcher | final-list_cand*.txt | fusion-catcher_final |
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215 +-------------------+-----------------------+-------------------------------------+
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216 |FusionMap | | fusionmap |
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217 +-------------------+-----------------------+-------------------------------------+
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218 |Trinity + GMAP | | trinity-gmap |
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219 +-------------------+-----------------------+-------------------------------------+
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220 |OncoFuse | | oncofuse |
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221 +-------------------+-----------------------+-------------------------------------+
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222 |RNA STAR | Chimeric.out.junction | rna-star_chimeric |
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223 +-------------------+-----------------------+-------------------------------------+
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224 |STAR Fusion | _candidates.final | star-fusion_final |
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225 +-------------------+-----------------------+-------------------------------------+
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226 |TopHat Fusion pre | fusions.out | tophat-fusion_pre |
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227 +-------------------+-----------------------+-------------------------------------+
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228 |TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion |
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229 +-------------------+-----------------------+-------------------------------------+
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230 |TopHat Fusion post | result.txt | tophat-fusion_post_result |
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231 +-------------------+-----------------------+-------------------------------------+
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232 |TopHat Fusion post | result.html | tophat-fusion_post_result_html |
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233 +-------------------+-----------------------+-------------------------------------+
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234
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235 To annotate genes upon the breakpoints you must provide a BED file that contains gene annotations for the user genome build. Make sure **your BED file contains one gene per line**. You should use BED files that contain one exon per line only if you want restrict your analysis to fusion genes detected within exons.
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236
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237 UCSC genome browser provides a very simple way of obtaining BED files with one gene per line by selecting their *RefSeq Genes*-track and *knownGene*-table and putting the export format to BED. Galaxy should have a built-in UCSC table browser.
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238
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239 ]]></help>
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240
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241 <citations>
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242 <citation type="bibtex">
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243 @unpublished{fuma,
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244 author = {Youri Hoogstrate},
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245 title = {FuMa: reporting overlap in RNA-seq detected fusion genes},
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246 url = { https://github.com/yhoogstrate/fuma }
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247 }
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248 </citation>
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249 </citations>
0
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250 </tool>