Mercurial > repos > melissacline > ucsc_xena_platform
comparison xena_import.xml @ 18:154a9b440b63
Updated the xena jar to version 14, updated the URL of the Xena pages
| author | melissacline |
|---|---|
| date | Tue, 02 Jun 2015 14:55:55 -0700 |
| parents | d57b5b3af15c |
| children | d8dc482ef970 |
comparison
equal
deleted
inserted
replaced
| 17:6785e729c7ad | 18:154a9b440b63 |
|---|---|
| 30 </command> | 30 </command> |
| 31 <inputs> | 31 <inputs> |
| 32 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> | 32 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> |
| 33 <conditional name="source"> | 33 <conditional name="source"> |
| 34 <param type="select" name="metadataSource" label="Metadata entry"> | 34 <param type="select" name="metadataSource" label="Metadata entry"> |
| 35 <option value="entry">Enter your own</option> | |
| 35 <option value="json">Specify json metadata file</option> | 36 <option value="json">Specify json metadata file</option> |
| 36 <option value="entry">Enter your own</option> | |
| 37 </param> | 37 </param> |
| 38 <when value="json"> | 38 <when value="json"> |
| 39 <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/> | 39 <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/> |
| 40 </when> | 40 </when> |
| 41 <when value="entry"> | 41 <when value="entry"> |
| 42 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> | 42 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> |
| 43 <conditional name="format"> | 43 <conditional name="format"> |
| 44 <param type="select" name="metadataType" label="File Format"> | 44 <param type="select" name="metadataType" label="File Format"> |
| 45 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples)</option> | 45 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option> |
| 46 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers)</option> | 46 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option> |
| 47 <option value="mutationVector">Mutation By Position</option> | 47 <option value="mutationVector">Mutation By Position</option> |
| 48 </param> | 48 </param> |
| 49 <when value="genomicMatrix"> | 49 <when value="genomicMatrix"> |
| 50 <conditional name="isCustom"> | 50 <conditional name="isCustom"> |
| 51 <param type="select" name="dataSubType" label="Type of data"> | 51 <param type="select" name="dataSubType" label="Type of data"> |
| 55 <option value="DNA methylation">DNA methylation</option> | 55 <option value="DNA methylation">DNA methylation</option> |
| 56 <option value="exon expression">exon expression</option> | 56 <option value="exon expression">exon expression</option> |
| 57 <option value="gene expression">gene expression</option> | 57 <option value="gene expression">gene expression</option> |
| 58 <option value="gene expression RNAseq">gene expression RNAseq</option> | 58 <option value="gene expression RNAseq">gene expression RNAseq</option> |
| 59 <option value="gene expression Array">gene expression Array</option> | 59 <option value="gene expression Array">gene expression Array</option> |
| 60 <option value="mRNA expression">mRNA expression</option> | |
| 60 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> | 61 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> |
| 61 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> | 62 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> |
| 62 <option value="protein expression RPPA">protein expression RPPA</option> | 63 <option value="protein expression RPPA">protein expression RPPA</option> |
| 63 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option> | 64 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option> |
| 64 </param> | 65 </param> |
| 70 <when value="DNA methylation"/> | 71 <when value="DNA methylation"/> |
| 71 <when value="exon expression"/> | 72 <when value="exon expression"/> |
| 72 <when value="gene expression"/> | 73 <when value="gene expression"/> |
| 73 <when value="gene expression RNAseq"/> | 74 <when value="gene expression RNAseq"/> |
| 74 <when value="gene expression Array"/> | 75 <when value="gene expression Array"/> |
| 76 <when value="mRNA expression"/> | |
| 75 <when value="somatic mutation (SNP and small INDELs)"/> | 77 <when value="somatic mutation (SNP and small INDELs)"/> |
| 76 <when value="somatic mutation (gene level)"/> | 78 <when value="somatic mutation (gene level)"/> |
| 77 <when value="protein expression RPPA"/> | 79 <when value="protein expression RPPA"/> |
| 78 <when value="PARADIGM pathway activity"/> | 80 <when value="PARADIGM pathway activity"/> |
| 79 </conditional> | 81 </conditional> |
| 87 <option value="DNA methylation">DNA methylation</option> | 89 <option value="DNA methylation">DNA methylation</option> |
| 88 <option value="exon expression">exon expression</option> | 90 <option value="exon expression">exon expression</option> |
| 89 <option value="gene expression">gene expression</option> | 91 <option value="gene expression">gene expression</option> |
| 90 <option value="gene expression RNAseq">gene expression RNAseq</option> | 92 <option value="gene expression RNAseq">gene expression RNAseq</option> |
| 91 <option value="gene expression Array">gene expression Array</option> | 93 <option value="gene expression Array">gene expression Array</option> |
| 94 <option value="mRNA expression">mRNA expression</option> | |
| 92 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> | 95 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> |
| 93 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> | 96 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> |
| 94 <option value="protein expression RPPA">protein expression RPPA</option> | 97 <option value="protein expression RPPA">protein expression RPPA</option> |
| 95 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option> | 98 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option> |
| 96 </param> | 99 </param> |
| 102 <when value="DNA methylation"/> | 105 <when value="DNA methylation"/> |
| 103 <when value="exon expression"/> | 106 <when value="exon expression"/> |
| 104 <when value="gene expression"/> | 107 <when value="gene expression"/> |
| 105 <when value="gene expression RNAseq"/> | 108 <when value="gene expression RNAseq"/> |
| 106 <when value="gene expression Array"/> | 109 <when value="gene expression Array"/> |
| 110 <when value="mRNA expression"/> | |
| 107 <when value="somatic mutation (SNP and small INDELs)"/> | 111 <when value="somatic mutation (SNP and small INDELs)"/> |
| 108 <when value="somatic mutation (gene level)"/> | 112 <when value="somatic mutation (gene level)"/> |
| 109 <when value="protein expression RPPA"/> | 113 <when value="protein expression RPPA"/> |
| 110 <when value="PARADIGM pathway activity"/> | 114 <when value="PARADIGM pathway activity"/> |
| 111 </conditional> | 115 </conditional> |
| 119 </inputs> | 123 </inputs> |
| 120 <outputs> | 124 <outputs> |
| 121 <data format="txt" name="outfile"/> | 125 <data format="txt" name="outfile"/> |
| 122 </outputs> | 126 </outputs> |
| 123 <help> | 127 <help> |
| 124 To Appear soon... | 128 To Appear, soon... |
| 125 </help> | 129 </help> |
| 126 </tool> | 130 </tool> |