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1 <tool id="igvscreenshot" name="Take an IGV screenshot" version="1.2">
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2
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3 <description>specifying tracks and a genomic location</description>
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4
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5 <requirements>
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6 <requirement type="package" version="2.3.57">igv</requirement>
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7 </requirements>
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8
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9
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10 <command interpreter="bash">
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11 igvscreenshot.sh
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12 --build $reference
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13 #for $i, $t in enumerate( $tracks )
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14 --track ${t.inputfile}
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15 --ftype ${t.inputfile.extension}
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16 --view ${t.view}
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17 --viewaspairs ${t.viewaspairs}
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18 #if not $t.trackname <!-- validator for empty field does not seem to work within a repeat, so this is the workaround -->
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19 #set $tracklabel = "noname"
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20 #else
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21 #set $tracklabel = $t.trackname
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22 #end if
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23 --label $tracklabel
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24 #if $t.inputfile.extension == "bam"
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25 --index $t.inputfile.metadata.bam_index
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26 #else
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27 --index "none"
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28 #end if
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29 #end for
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30 --region "$region"
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31 </command>
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32
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33
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34 <inputs>
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35 <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions -->
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36
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37 <param name="reference" type="select" label="Select Build">
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38 <option value="hg18"> hg18 </option>
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39 <option value="hg19"> hg19 </option>
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40 </param>
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41
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42 <!-- file from history -->
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43 <repeat name="tracks" title="Track" min="1">
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44 <param name="inputfile" type="data" format="bam,vcf,bed,gtf,gff" label="Select input file" help="choose input file from history"/>
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45 <param name="trackname" type="text" size="100" value="track label" label="Track Label" >
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46 <sanitizer>
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47 <valid initial="default">
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48 <add preset="string.printable"/>
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49 <remove value=" "/>
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50 </valid>
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51 <mapping initial="none">
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52 <add source=" " target="_"/>
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53 </mapping>
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54 </sanitizer>
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55 </param>
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56 <param name="view" type="select" label="View settings of track" >
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57 <option value="collapse" > collapsed </option>
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58 <option value="expand" > expanded </option>
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59 <option value="squish" > squished </option>
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60 </param>
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61 <param name="viewaspairs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="view as pairs?" help="optional setting for paired-end data"/>
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62
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63 </repeat>
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64 <!-- text field parameter -->
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65 <param name="region" type="text" size="100" value="chr:start-end" label="Enter region to visualise in IGV, format chr:start-end" help="to show multiple regions in a single image, use comma-separated list of regions, e.g. chr1:0-100,chr2:100-200"/>
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66
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67 </inputs>
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68
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69
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70 <outputs>
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71 <data format="png" name="outputfile" from_work_dir="screenshot.png" label="IGV screenshot of region ${region} on ${on_string}"/>
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72 </outputs>
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73
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74 <help>
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75 This tool will create an IGV screenshot of the desired location(s) with the desired tracks.
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76
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77 Tracks may be bam, vcf, bed, gff or gtf format.
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78
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79 Multiple regions may be specified (comma-separated)
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80
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81
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82
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83 </help>
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84 </tool> |
