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1 <tool id="xenaImport" description="Import into XENA from Galaxy" name="XENA Import" version="0.0.1">
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2 <description>Import from Galaxy into the Xena VM</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">installXena</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 xena_import.py ${xenaInputData} $outfile
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8 #if $source.metadataSource == "json"
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9 --json ${source.xenaMetadata}
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10 #else
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11 --cohort "${source.cohort}" --type ${source.format.metadataType}
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12 #if $source.format.metadataType == "genomicMatrix" or $source.format.metadataType == "clinicalMatrix":
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13 #if $source.format.isCustom.dataSubType == "custom"
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14 #if $source.format.isCustom.customSubType
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15 --dataSubType "${source.format.isCustom.customSubType}"
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16 #end if
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17 #else
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18 --dataSubType "${source.format.isCustom.dataSubType}"
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19 #end if
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20 #end if
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21 #if $source.label
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22 --label "${source.label}"
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23 #else
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24 --label "${xenaInputData.name}"
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25 #end if
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26 #end if
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27 </command>
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28 <inputs>
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29 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
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30 <conditional name="source">
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31 <param type="select" name="metadataSource" label="Metadata entry">
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32 <option value="json">Specify json metadata file</option>
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33 <option value="entry">Enter your own</option>
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34 </param>
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35 <when value="json">
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36 <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/>
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37 </when>
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38 <when value="entry">
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39 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
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40 <conditional name="format">
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41 <param type="select" name="metadataType" label="File Format">
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42 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples)</option>
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43 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers)</option>
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44 <option value="mutationVector">Mutation By Position</option>
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45 </param>
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46 <when value="genomicMatrix">
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47 <conditional name="isCustom">
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48 <param type="select" name="dataSubType" label="Type of data">
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49 <option value="custom">Enter your own</option>
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50 <option value="phenotype">phenotype</option>
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51 <option value="copy number">copy number</option>
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52 <option value="DNA methylation">DNA methylation</option>
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53 <option value="exon expression">exon expression</option>
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54 <option value="gene expression">gene expression</option>
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55 <option value="gene expression RNAseq">gene expression RNAseq</option>
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56 <option value="gene expression Array">gene expression Array</option>
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57 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
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58 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
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59 <option value="protein expression RPPA">protein expression RPPA</option>
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60 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
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61 </param>
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62 <when value="custom">
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63 <param type="text" name="customSubType" label="Type of data" optional="true"/>
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64 </when>
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65 <when value="phenotype"/>
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66 <when value="copy number"/>
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67 <when value="DNA methylation"/>
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68 <when value="exon expression"/>
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69 <when value="gene expression"/>
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70 <when value="gene expression RNAseq"/>
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71 <when value="gene expression Array"/>
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72 <when value="somatic mutation (SNP and small INDELs)"/>
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73 <when value="somatic mutation (gene level)"/>
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74 <when value="protein expression RPPA"/>
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75 <when value="PARADIGM pathway activity"/>
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76 </conditional>
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77 </when>
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78 <when value="clinicalMatrix">
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79 <conditional name="isCustom">
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80 <param type="select" name="dataSubType" label="Type of data">
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81 <option value="custom">Enter your own</option>
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82 <option value="phenotype">phenotype</option>
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83 <option value="copy number">copy number</option>
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84 <option value="DNA methylation">DNA methylation</option>
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85 <option value="exon expression">exon expression</option>
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86 <option value="gene expression">gene expression</option>
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87 <option value="gene expression RNAseq">gene expression RNAseq</option>
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88 <option value="gene expression Array">gene expression Array</option>
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89 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
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90 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
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91 <option value="protein expression RPPA">protein expression RPPA</option>
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92 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
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93 </param>
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94 <when value="custom">
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95 <param type="text" name="customSubType" label="Type of data" optional="true"/>
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96 </when>
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97 <when value="phenotype"/>
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98 <when value="copy number"/>
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99 <when value="DNA methylation"/>
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100 <when value="exon expression"/>
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101 <when value="gene expression"/>
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102 <when value="gene expression RNAseq"/>
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103 <when value="gene expression Array"/>
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104 <when value="somatic mutation (SNP and small INDELs)"/>
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105 <when value="somatic mutation (gene level)"/>
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106 <when value="protein expression RPPA"/>
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107 <when value="PARADIGM pathway activity"/>
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108 </conditional>
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109 </when>
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110 <when value="mutationVector"/>
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111 </conditional>
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112 <param type="text" name="label" label="Display Name (Optional)" optional="true"/>
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113 </when>
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114 </conditional>
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115 </inputs>
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116 <outputs>
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117 <data format="txt" name="outfile"/>
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118 </outputs>
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119 <help>
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120 To Appear soon...
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121 </help>
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122 </tool>
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