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1 <tool id="circosJunctions" name="Integrative Plot" version="1.56">
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2 <description> Create a Circos plot with Complete Genomics and/or SNParray data </description>
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3
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4
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5 <requirements>
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6 <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
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7 <requirement type="package" version="0.64">circos</requirement>
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8 </requirements>
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9
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10
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11 <command interpreter="bash">
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12 galaxy_runCircos.sh
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13 $junctions
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14 $probes
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15 $snps
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16 $variants
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17 #if $imageformat == "png"
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18 $wg_out
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19 $montage_out
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20 #else
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21 $wg_out2
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22 $montage_out2
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23 #end if
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24 $chromosomes_out
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25 $reference
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26 $custom_out
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27 "$custom.region"
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28 $genetrack
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29 $imageformat
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30 \$CIRCOS_SCRIPT_PATH/scripts
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31 \$CIRCOS_SCRIPT_PATH/config
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32 </command>
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33
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34 <inputs>
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35
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36 <param name="reference" type="select" label="Reference">
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37 <option value="hg18" selected="true"> HG18 (build 36) </option>
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38 <option value="hg19"> HG19 (build 37) </option>
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39 </param>
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40 <param name="junctions" type="data" optional="true" format="tabular" label="CG Junctions file"/>
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41 <param name="variants" type="data" optional="true" format="tabular" label="Variants list (e.g. output from CG listvariants)"/>
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42
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43 <param name="snps" type="data" optional="true" format="tabular" label="Illumina (Nexus) snps.txt file"/>
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44 <param name="probes" type="data" optional="true" format="tabular" label="Illumina (Nexus) probes.txt file"/>
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45
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46 <param name="wg" type="boolean" truevalue="Y" falsevalue="N" checked="true" label="Generate Whole-Genome plot?"/>
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47 <param name="chrplots" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="Also generate per-chromosome plots?"/>
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48 <param name="montage" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="Also generate montage of per-chromosome plots?"/>
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49 <param name="genetrack" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Add ImpactedGenes track (only for the per-chromosome or custom plots)" help="Shows which genes are impacted by the SV events (junctions)"/>
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50
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51 <conditional name="custom">
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52 <param name="plot" type="select" label="Create a plot of a custom region?">
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53 <option value="N" selected="true"> No </option>
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54 <option value="Y"> Yes </option>
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55 </param>
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56 <when value="N">
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57 <param name="region" type="hidden" value="None" />
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58 </when>
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59 <when value="Y">
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60 <param name="region" type="text" value="None" label="Region" help="For example: 'chr5;chr6;chrX' or 'chr12:12345-34567' or 'chr5:0-100,200-333;chrX:34567-78347'">
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61 <sanitizer sanitize="False"/>
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62 </param>
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63 </when>
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64 </conditional>
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65
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66 <param name="imageformat" type="select" label="Image Format">
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67 <option value="png" selected="true"> PNG </option>
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68 <option value="svg"> SVG </option>
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69 </param>
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70
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71 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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72
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73 </inputs>
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74
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75 <outputs>
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76 <data format="png" name="wg_out" label="Whole genome plot on ${on_string}"> <filter> imageformat == "png" </filter> <filter> wg </filter> </data>
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77 <data format="png" name="montage_out" label="Chromosomes_montage on ${on_string}"> <filter> imageformat == "png" </filter> <filter> montage </filter> </data>
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78 <data format="png" name="custom_out" label="Plot of region ${custom.region} on ${on_string} "> <filter> imageformat == "png" </filter> <filter> custom['plot'] == "Y" </filter> </data>
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79
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80 <data format="svg" name="wg_out2" label="Whole genome plot on ${on_string}"> <filter> imageformat == "svg" </filter> <filter> wg </filter> </data>
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81 <data format="svg" name="montage_out2" label="Chromosomes_montage on ${on_string}"> <filter> imageformat == "svg" </filter> <filter> montage </filter> </data>
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82 <data format="svg" name="custom_out2" label="Plot of region ${custom.region} on ${on_string} "> <filter> imageformat == "svg" </filter> <filter> custom['plot'] == "Y" </filter> </data>
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83
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84
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85 <data format="gzip" name="chromosomes_out" label="Chromosome plots on ${on_string}"> <filter> chrplots </filter> </data>
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86 </outputs>
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87
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88 <help>
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89
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90
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91 </help>
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92
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93 </tool>
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94
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95
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