comparison xena_import.xml @ 5:c5b71ce5f7b1

Tweaking the xena import options - for a second time (grrr)
author melissacline
date Wed, 11 Feb 2015 17:15:22 -0800
parents 6eeb3ca663fb
children a1cad00d45ff
comparison
equal deleted inserted replaced
3:98b498545a52 5:c5b71ce5f7b1
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">
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>