Mercurial > repos > melissacline > ucsc_xena_platform
comparison xena_import.xml @ 49:8da6920a39ac
add hg19 assembly in xena_import
| author | jingchunzhu |
|---|---|
| date | Sun, 09 Aug 2015 23:23:58 -0700 |
| parents | d717d0c4c8f1 |
| children |
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| 48:d717d0c4c8f1 | 49:8da6920a39ac |
|---|---|
| 24 | 24 |
| 25 #if $format.metadataType == "genomicMatrix" and $format.withProbeMap.probeMap =="select" | 25 #if $format.metadataType == "genomicMatrix" and $format.withProbeMap.probeMap =="select" |
| 26 --probeMap "${format.withProbeMap.probeMapFile}" | 26 --probeMap "${format.withProbeMap.probeMapFile}" |
| 27 #end if | 27 #end if |
| 28 | 28 |
| 29 #if $colNormalization: | 29 #if $format.metadataType == "genomicMatrix" and $format.colNormalization: |
| 30 --colNormalization 1 | 30 --colNormalization 1 |
| 31 #end if | 31 #end if |
| 32 | |
| 33 #if $format.metadataType == "mutationVector" and $format.assembly: | |
| 34 --assembly "${format.assembly}" | |
| 35 #end if | |
| 36 | |
| 32 </command> | 37 </command> |
| 33 <inputs> | 38 <inputs> |
| 34 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> | 39 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> |
| 35 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> | 40 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> |
| 36 <conditional name="format"> | 41 <conditional name="format"> |
| 79 <when value="somatic mutation (SNP and small INDELs)"/> | 84 <when value="somatic mutation (SNP and small INDELs)"/> |
| 80 <when value="somatic mutation (gene level)"/> | 85 <when value="somatic mutation (gene level)"/> |
| 81 <when value="protein expression RPPA"/> | 86 <when value="protein expression RPPA"/> |
| 82 <when value="PARADIGM pathway activity"/> | 87 <when value="PARADIGM pathway activity"/> |
| 83 </conditional> | 88 </conditional> |
| 84 | 89 |
| 90 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> | |
| 85 </when> | 91 </when> |
| 92 | |
| 86 <when value="clinicalMatrix"> | 93 <when value="clinicalMatrix"> |
| 87 <conditional name="isCustom"> | 94 <conditional name="isCustom"> |
| 88 <param type="select" name="dataSubType" label="Type of data"> | 95 <param type="select" name="dataSubType" label="Type of data"> |
| 89 <option value="custom">Enter your own</option> | 96 <option value="custom">Enter your own</option> |
| 90 <option value="phenotype">phenotype</option> | 97 <option value="phenotype">phenotype</option> |
| 93 <param type="text" name="customSubType" label="Type of data" optional="true"/> | 100 <param type="text" name="customSubType" label="Type of data" optional="true"/> |
| 94 </when> | 101 </when> |
| 95 <when value="phenotype"/> | 102 <when value="phenotype"/> |
| 96 </conditional> | 103 </conditional> |
| 97 </when> | 104 </when> |
| 98 <when value="mutationVector"/> | 105 |
| 106 <when value="mutationVector"> | |
| 107 <param type="select" name="assembly" label ="assembly"> | |
| 108 <option value = "hg19"> hg19</option> | |
| 109 </param> | |
| 110 </when> | |
| 99 </conditional> | 111 </conditional> |
| 100 <param type="text" name="label" label="Display Name (Optional)" optional="true"/> | 112 <param type="text" name="label" label="Display Name (Optional)" optional="true"/> |
| 101 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> | |
| 102 </inputs> | 113 </inputs> |
| 103 <outputs> | 114 <outputs> |
| 104 <data format="txt" name="outfile"/> | 115 <data format="txt" name="outfile"/> |
| 105 </outputs> | 116 </outputs> |
| 106 <help> | 117 <help> |