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annotate fuma.xml @ 0:a4cfaa0e3e5d draft

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author yhoogstrate
date Thu, 21 May 2015 09:56:41 -0400
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="fuma" name="FuMa" version="2.7.1.b">
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3 <description>FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).</description>
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4
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5 <requirements>
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6 <requirement type="package" version="2.7.1">fuma</requirement>
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7 </requirements>
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9 <version_command>fuma --version 2>&amp;1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->
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10
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11 <command>
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12 #import pipes
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13
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14 #set $gene_annotations = []
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15 #set $samples = []
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16 #set $links = []
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18 #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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23
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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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31
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32 fuma
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33 -a
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34 $gene_annotations_str
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35 -s
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36 $samples_str
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37 -l
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38 $links_str
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39 #if $output_format.value == "list_boolean"
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40 -f list
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41 #else
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42 -f $output_format.value
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43 #end if
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44 -o $fuma_overview ;
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45
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46
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47
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48 #if $output_format.value == "list_boolean"
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49 fuma-list-to-boolean-list -o tmp.txt $fuma_overview &amp;&amp;
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50 mv tmp.txt $fuma_overview
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51 #end if
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52 </command>
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53
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54 <inputs>
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55 <repeat name="datasets" title="FusionGene Datasets" min="2">
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56 <param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />
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57 <param name="format" type="select" label="Format of dataset">
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58 <option value="chimerascan">ChimeraScan</option>
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59 <option value="defuse">DeFuse</option>
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60 <option value="complete-genomics">Complete Genomics</option>
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61 <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>
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62 <option value="fusionmap">FusionMap</option>
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63 <option value="trinity-gmap">GMAP (As step after Trinity)</option>
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64 <option value="oncofuse">OncoFuse</option>
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65 <option value="rna-star_chimeric">STAR (chimeric file)</option>
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66 <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>
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67 <option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>
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68 <option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>
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69 </param>
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70 <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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71 </repeat>
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72
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73 <param name="output_format" type="select" label="Output format">
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74 <option value="list_boolean" selected="true">List (Boolean)</option>
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75 <option value="list">List</option>
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76 <option value="summary">Count summary</option>
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77 </param>
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78 </inputs>
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79
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80 <outputs>
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81 <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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82 </outputs>
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83
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84 <tests>
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85 <test>
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86 <!-- <repeat name="datasets"> -->
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87 <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" />
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88 <param name="datasets_0|format" value="chimerascan" />
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89 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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90 <!-- </repeat> -->
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91 <!-- <repeat name="datasets"> -->
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92 <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" />
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93 <param name="datasets_1|format" value="defuse" />
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94 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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95 <!-- </repeat> -->
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96 <!-- <repeat name="datasets"> -->
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97 <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" />
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98 <param name="datasets_2|format" value="fusionmap" />
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99 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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100 <!-- </repeat> -->
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101 <!-- <repeat name="datasets"> -->
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102 <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" />
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103 <param name="datasets_3|format" value="fusionmap" />
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104 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
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105 <!-- </repeat> -->
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106
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107 <param name="output_format" value="summary" />
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108
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109 <output name="fuma_overview" file="output.txt" />
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110 </test>
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111 </tests>
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112
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113 <help>============
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114 Introduction
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115 ============
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116
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117 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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118
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119 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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120
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121 =====
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122 Usage
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123 =====
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124
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125 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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126
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127 *******
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128 Formats
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129 *******
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130
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131 +-------------------+-----------------------+-------------------------------------+
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132 |Tools | File | Format string |
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133 +===================+=======================+=====================================+
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134 |ChimeraScan | chimeras.bedpe | chimerascan |
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135 +-------------------+-----------------------+-------------------------------------+
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136 |Complete Genomics | highConfidenceJu*.tsv | complete-genomics |
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137 +-------------------+-----------------------+-------------------------------------+
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138 |Complete Genomics | allJunctionsBeta*.tsv | complete-genomics |
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139 +-------------------+-----------------------+-------------------------------------+
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140 |DeFuse | results.txt | defuse |
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141 +-------------------+-----------------------+-------------------------------------+
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142 |DeFuse | results.classify.txt | defuse |
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143 +-------------------+-----------------------+-------------------------------------+
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144 |DeFuse | results.filtered.txt | defuse |
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145 +-------------------+-----------------------+-------------------------------------+
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146 |Fusion Catcher | final-list_cand*.txt | fusion-catcher_final |
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147 +-------------------+-----------------------+-------------------------------------+
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148 |FusionMap | | fusionmap |
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149 +-------------------+-----------------------+-------------------------------------+
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150 |Trinity + GMAP | | trinity-gmap |
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151 +-------------------+-----------------------+-------------------------------------+
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152 |OncoFuse | | oncofuse |
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153 +-------------------+-----------------------+-------------------------------------+
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154 |RNA STAR | Chimeric.out.junction | rna-star_chimeric |
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155 +-------------------+-----------------------+-------------------------------------+
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156 |TopHat Fusion pre | fusions.out | tophat-fusion_pre |
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157 +-------------------+-----------------------+-------------------------------------+
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158 |TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion |
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159 +-------------------+-----------------------+-------------------------------------+
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160 |TopHat Fusion post | result.txt | tophat-fusion_post_result |
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161 +-------------------+-----------------------+-------------------------------------+
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162
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163 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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164
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165 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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167 </help>
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168 </tool>