Mercurial > repos > melissacline > ucsc_xena_platform
annotate xena_import.xml @ 49:8da6920a39ac
add hg19 assembly in xena_import
author | jingchunzhu |
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date | Sun, 09 Aug 2015 23:23:58 -0700 |
parents | d717d0c4c8f1 |
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rev | line source |
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1 <tool id="xenaImport" name="XENA Import" version="0.0.1"> |
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Download data from any hub in the federated xena platform
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2 <description>Load a Galaxy dataset into the Xena Server running on this galaxy instance</description> |
0 | 3 <requirements> |
4 <requirement type="package" version="1.0">installXena</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
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}" |
0 | 13 #end if |
14 #else | |
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15 --dataSubType "${format.isCustom.dataSubType}" |
0 | 16 #end if |
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 |
48 | 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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28 |
49 | 29 #if $format.metadataType == "genomicMatrix" and $format.colNormalization: |
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30 --colNormalization 1 |
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31 #end if |
49 | 32 |
33 #if $format.metadataType == "mutationVector" and $format.assembly: | |
34 --assembly "${format.assembly}" | |
35 #end if | |
36 | |
0 | 37 </command> |
38 <inputs> | |
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> |
0 | 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> |
49 | 89 |
90 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> | |
0 | 91 </when> |
49 | 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> |
0 | 104 </when> |
49 | 105 |
106 <when value="mutationVector"> | |
107 <param type="select" name="assembly" label ="assembly"> | |
108 <option value = "hg19"> hg19</option> | |
109 </param> | |
110 </when> | |
0 | 111 </conditional> |
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112 <param type="text" name="label" label="Display Name (Optional)" optional="true"/> |
0 | 113 </inputs> |
114 <outputs> | |
115 <data format="txt" name="outfile"/> | |
116 </outputs> | |
117 <help> | |
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118 To Appear, soon... |
0 | 119 </help> |
120 </tool> |