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comparison xena_import.xml @ 35:d8dc482ef970

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add functionality to import probeMap
author jingchunzhu <jingchunzhu@gmail.com>
date Thu, 23 Jul 2015 16:14:33 -0700
parents d57b5b3af15c
children 066ae9df2d27
comparison
equal deleted inserted replaced
34:a3fbe077a14c 35:d8dc482ef970
1 <tool id="xenaImport" description="Import into XENA from Galaxy" name="XENA Import" version="0.0.1"> 1 <tool id="xenaImport" name="XENA Import" version="0.0.1">
2 <description>Import from Galaxy into the Xena VM</description> 2 <description>Import from Galaxy into the Xena VM</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0">installXena</requirement> 4 <requirement type="package" version="1.0">installXena</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 xena_import.py ${xenaInputData} $outfile 7 xena_import.py ${xenaInputData} $outfile
8 #if $source.metadataSource == "json" 8 --cohort "${cohort}" --type ${format.metadataType}
9 --json ${source.xenaMetadata} 9 #if $format.metadataType == "genomicMatrix" or $format.metadataType == "clinicalMatrix":
10 #else 10 #if $format.isCustom.dataSubType == "custom"
11 --cohort "${source.cohort}" --type ${source.format.metadataType} 11 #if $format.isCustom.customSubType
12 #if $source.format.metadataType == "genomicMatrix" or $source.format.metadataType == "clinicalMatrix": 12 --dataSubType "${format.isCustom.customSubType}"
13 #if $source.format.isCustom.dataSubType == "custom"
14 #if $source.format.isCustom.customSubType
15 --dataSubType "${source.format.isCustom.customSubType}"
16 #end if
17 #else
18 --dataSubType "${source.format.isCustom.dataSubType}"
19 #end if 13 #end if
20 #end if
21 #if $source.label
22 --label "${source.label}"
23 #else 14 #else
24 --label "${xenaInputData.name}" 15 --dataSubType "${format.isCustom.dataSubType}"
25 #end if 16 #end if
26 #end if 17 #end if
18
19 #if $label
20 --label "${label}"
21 #else
22 --label "${xenaInputData.name}"
23 #end if
24
25 #if $format.withProbeMap.probeMap =="select"
26 --probeMap "${format.withProbeMap.probeMapFile}"
27 #end if
28
27 #if $colNormalization: 29 #if $colNormalization:
28 --colNormalization 1 30 --colNormalization 1
29 #end if 31 #end if
30 </command> 32 </command>
31 <inputs> 33 <inputs>
32 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> 34 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
33 <conditional name="source"> 35 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
34 <param type="select" name="metadataSource" label="Metadata entry"> 36 <conditional name="format">
35 <option value="entry">Enter your own</option> 37 <param type="select" name="metadataType" label="File Format">
36 <option value="json">Specify json metadata file</option> 38 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option>
39 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option>
40 <option value="mutationVector">Mutation By Position</option>
37 </param> 41 </param>
38 <when value="json"> 42 <when value="genomicMatrix">
39 <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/> 43 <conditional name="withProbeMap">
44 <param type="select" name="probeMap" label="Identifier to Gene Mapping">
45 <option value="none">No id to gene mapping file</option>
46 <option value="select">Select a id to gene mapping file</option>
47 </param>
48 <when value="none"/>
49 <when value="select">
50 <param type="data" format="tabular" multiple="false" name="probeMapFile" optional="false"/>
51 </when>
52 </conditional>
53
54 <conditional name="isCustom">
55 <param type="select" name="dataSubType" label="Type of data">
56 <option value="custom">Enter your own</option>
57 <option value="copy number">copy number</option>
58 <option value="DNA methylation">DNA methylation</option>
59 <option value="exon expression">exon expression</option>
60 <option value="gene expression">gene expression</option>
61 <option value="gene expression RNAseq">gene expression RNAseq</option>
62 <option value="gene expression Array">gene expression Array</option>
63 <option value="mRNA expression">mRNA expression</option>
64 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
65 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
66 <option value="protein expression RPPA">protein expression RPPA</option>
67 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
68 </param>
69 <when value="custom">
70 <param type="text" name="customSubType" label="Type of data" optional="true"/>
71 </when>
72 <when value="copy number"/>
73 <when value="DNA methylation"/>
74 <when value="exon expression"/>
75 <when value="gene expression"/>
76 <when value="gene expression RNAseq"/>
77 <when value="gene expression Array"/>
78 <when value="mRNA expression"/>
79 <when value="somatic mutation (SNP and small INDELs)"/>
80 <when value="somatic mutation (gene level)"/>
81 <when value="protein expression RPPA"/>
82 <when value="PARADIGM pathway activity"/>
83 </conditional>
84
40 </when> 85 </when>
41 <when value="entry"> 86 <when value="clinicalMatrix">
42 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> 87 <conditional name="isCustom">
43 <conditional name="format"> 88 <param type="select" name="dataSubType" label="Type of data">
44 <param type="select" name="metadataType" label="File Format"> 89 <option value="custom">Enter your own</option>
45 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option> 90 <option value="phenotype">phenotype</option>
46 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option> 91 </param>
47 <option value="mutationVector">Mutation By Position</option> 92 <when value="custom">
48 </param> 93 <param type="text" name="customSubType" label="Type of data" optional="true"/>
49 <when value="genomicMatrix"> 94 </when>
50 <conditional name="isCustom"> 95 <when value="phenotype"/>
51 <param type="select" name="dataSubType" label="Type of data"> 96 </conditional>
52 <option value="custom">Enter your own</option>
53 <option value="phenotype">phenotype</option>
54 <option value="copy number">copy number</option>
55 <option value="DNA methylation">DNA methylation</option>
56 <option value="exon expression">exon expression</option>
57 <option value="gene expression">gene expression</option>
58 <option value="gene expression RNAseq">gene expression RNAseq</option>
59 <option value="gene expression Array">gene expression Array</option>
60 <option value="mRNA expression">mRNA expression</option>
61 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
62 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
63 <option value="protein expression RPPA">protein expression RPPA</option>
64 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
65 </param>
66 <when value="custom">
67 <param type="text" name="customSubType" label="Type of data" optional="true"/>
68 </when>
69 <when value="phenotype"/>
70 <when value="copy number"/>
71 <when value="DNA methylation"/>
72 <when value="exon expression"/>
73 <when value="gene expression"/>
74 <when value="gene expression RNAseq"/>
75 <when value="gene expression Array"/>
76 <when value="mRNA expression"/>
77 <when value="somatic mutation (SNP and small INDELs)"/>
78 <when value="somatic mutation (gene level)"/>
79 <when value="protein expression RPPA"/>
80 <when value="PARADIGM pathway activity"/>
81 </conditional>
82 </when>
83 <when value="clinicalMatrix">
84 <conditional name="isCustom">
85 <param type="select" name="dataSubType" label="Type of data">
86 <option value="custom">Enter your own</option>
87 <option value="phenotype">phenotype</option>
88 <option value="copy number">copy number</option>
89 <option value="DNA methylation">DNA methylation</option>
90 <option value="exon expression">exon expression</option>
91 <option value="gene expression">gene expression</option>
92 <option value="gene expression RNAseq">gene expression RNAseq</option>
93 <option value="gene expression Array">gene expression Array</option>
94 <option value="mRNA expression">mRNA expression</option>
95 <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option>
96 <option value="somatic mutation (gene level)">somatic mutation (gene level)</option>
97 <option value="protein expression RPPA">protein expression RPPA</option>
98 <option value="PARADIGM pathway activity">PARADIGM pathway activity</option>
99 </param>
100 <when value="custom">
101 <param type="text" name="customSubType" label="Type of data" optional="true"/>
102 </when>
103 <when value="phenotype"/>
104 <when value="copy number"/>
105 <when value="DNA methylation"/>
106 <when value="exon expression"/>
107 <when value="gene expression"/>
108 <when value="gene expression RNAseq"/>
109 <when value="gene expression Array"/>
110 <when value="mRNA expression"/>
111 <when value="somatic mutation (SNP and small INDELs)"/>
112 <when value="somatic mutation (gene level)"/>
113 <when value="protein expression RPPA"/>
114 <when value="PARADIGM pathway activity"/>
115 </conditional>
116 </when>
117 <when value="mutationVector"/>
118 </conditional>
119 <param type="text" name="label" label="Display Name (Optional)" optional="true"/>
120 </when> 97 </when>
98 <when value="mutationVector"/>
121 </conditional> 99 </conditional>
100 <param type="text" name="label" label="Display Name (Optional)" optional="true"/>
122 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> 101 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/>
123 </inputs> 102 </inputs>
124 <outputs> 103 <outputs>
125 <data format="txt" name="outfile"/> 104 <data format="txt" name="outfile"/>
126 </outputs> 105 </outputs>