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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="fuma" name="FuMa" version="2.6.6.a">
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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="2.6.6">fuma</requirement>
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7 </requirements>
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8
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9 <version_command>fuma --version</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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17
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18 #for $i, $d in enumerate( $datasets )
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19
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20 #set $sample_name = pipes.quote(str($d['sample'].name))
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21
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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 -f 'list'
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40 -o $fuma_overview
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41 </command>
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42
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43 <inputs>
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44 <repeat name="datasets" title="FusionGene Datasets" min="2">
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45 <param name="sample" type="data" format="txt, tabular" label="Dataset ()" />
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46 <param name="format" type="select" label="Format of dataset">
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47 <option value="chimerascan">ChimeraScan</option>
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48 <option value="defuse">DeFuse</option>
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49 <option value="completegenomics">Complete Genomics</option>
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50 <option value="tophatfusionpostpotentialfusion">Tophat Fusion Post (potential fusion file)</option>
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51 <option value="tophatfusionpostresult">Tophat Fusion Post (result file)</option>
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52 <option value="tophatfusionpre">Tophat Fusion Pre (final list file)</option>
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53 <option value="fusioncatcherfinal">FusionCatcher (final-list file)</option>
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54 <option value="fusionmap">FusionMap</option>
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55 <option value="rnastarchimeric">STAR (chimeric file)</option>
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56 <option value="oncofuse">Oncofuse</option>
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57 <option value="trinitygmap">GMAP (As step after Trinity)</option>
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58 </param>
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59 <param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene names if different gene names are being used." />
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60 </repeat>
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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="fuma_overview" label="${tool.name} on ${', '.join([ str(d['sample'].hid)+': '+d['sample'].name for d in $datasets ])}" />
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65 </outputs>
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66
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67 <help>
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68 </help>
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69 </tool>
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