Mercurial > repos > melissacline > ucsc_xena_platform

annotate xena_import.xml @ 55:421b18a0b659 default tip

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update v17 step 2, add xena.jar
author jingchunzhu
date Tue, 22 Sep 2015 10:07:51 -0700
parents 8da6920a39ac
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1 <tool id="xenaImport" name="XENA Import" version="0.0.1">
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2 <description>Load a Galaxy dataset into the Xena Server running on this galaxy instance</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} $outfile
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8 --cohort "${cohort}" --type ${format.metadataType}
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9 #if $format.metadataType == "genomicMatrix" or $format.metadataType == "clinicalMatrix":
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10 #if $format.isCustom.dataSubType == "custom"
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11 #if $format.isCustom.customSubType
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12 --dataSubType "${format.isCustom.customSubType}"
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13 #end if
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14 #else
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15 --dataSubType "${format.isCustom.dataSubType}"
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16 #end if
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17 #end if
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18
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19 #if $label
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20 --label "${label}"
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21 #else
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22 --label "${xenaInputData.name}"
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23 #end if
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24
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25 #if $format.metadataType == "genomicMatrix" and $format.withProbeMap.probeMap =="select"
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26 --probeMap "${format.withProbeMap.probeMapFile}"
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27 #end if
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29 #if $format.metadataType == "genomicMatrix" and $format.colNormalization:
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30 --colNormalization 1
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31 #end if
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33 #if $format.metadataType == "mutationVector" and $format.assembly:
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34 --assembly "${format.assembly}"
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35 #end if
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36
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37 </command>
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38 <inputs>
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39 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
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40 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
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41 <conditional name="format">
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42 <param type="select" name="metadataType" label="File Format">
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43 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option>
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44 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option>
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45 <option value="mutationVector">Mutation By Position</option>
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46 </param>
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47 <when value="genomicMatrix">
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48 <conditional name="withProbeMap">
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49 <param type="select" name="probeMap" label="Identifier to Gene Mapping">
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50 <option value="none">No id to gene mapping file</option>
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51 <option value="select">Select a id to gene mapping file</option>
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52 </param>
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53 <when value="none"/>
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54 <when value="select">
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55 <param type="data" format="tabular" multiple="false" name="probeMapFile" optional="false"/>
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56 </when>
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57 </conditional>
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58
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59 <conditional name="isCustom">
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60 <param type="select" name="dataSubType" label="Type of data">
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61 <option value="custom">Enter your own</option>
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62 <option value="copy number">copy number</option>
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63 <option value="DNA methylation">DNA methylation</option>
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64 <option value="exon expression">exon expression</option>
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65 <option value="gene expression">gene expression</option>
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66 <option value="gene expression RNAseq">gene expression RNAseq</option>
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67 <option value="gene expression Array">gene expression Array</option>
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68 <option value="mRNA expression">mRNA expression</option>
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69 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
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70 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
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71 <option value="protein expression RPPA">protein expression RPPA</option>
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72 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
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73 </param>
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74 <when value="custom">
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75 <param type="text" name="customSubType" label="Type of data" optional="true"/>
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76 </when>
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77 <when value="copy number"/>
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78 <when value="DNA methylation"/>
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79 <when value="exon expression"/>
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80 <when value="gene expression"/>
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81 <when value="gene expression RNAseq"/>
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82 <when value="gene expression Array"/>
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83 <when value="mRNA expression"/>
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84 <when value="somatic mutation (SNP and small INDELs)"/>
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85 <when value="somatic mutation (gene level)"/>
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86 <when value="protein expression RPPA"/>
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87 <when value="PARADIGM pathway activity"/>
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88 </conditional>
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89
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90 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/>
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91 </when>
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92
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93 <when value="clinicalMatrix">
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94 <conditional name="isCustom">
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95 <param type="select" name="dataSubType" label="Type of data">
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96 <option value="custom">Enter your own</option>
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97 <option value="phenotype">phenotype</option>
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98 </param>
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99 <when value="custom">
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100 <param type="text" name="customSubType" label="Type of data" optional="true"/>
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101 </when>
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102 <when value="phenotype"/>
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103 </conditional>
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104 </when>
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105
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106 <when value="mutationVector">
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107 <param type="select" name="assembly" label ="assembly">
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108 <option value = "hg19"> hg19</option>
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109 </param>
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110 </when>
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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 </inputs>
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114 <outputs>
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115 <data format="txt" name="outfile"/>
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116 </outputs>
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117 <help>
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118 To Appear, soon...
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119 </help>
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120 </tool>