Mercurial > repos > melissacline > ucsc_xena_platform
view xena_import.xml @ 24:975abd814626
Uploaded, to try to fix a merge problem.
author | melissacline |
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date | Tue, 02 Jun 2015 19:17:14 -0400 |
parents | d57b5b3af15c |
children | d8dc482ef970 |
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<tool id="xenaImport" description="Import into XENA from Galaxy" name="XENA Import" version="0.0.1"> <description>Import from Galaxy into the Xena VM</description> <requirements> <requirement type="package" version="1.0">installXena</requirement> </requirements> <command interpreter="python"> xena_import.py ${xenaInputData} $outfile #if $source.metadataSource == "json" --json ${source.xenaMetadata} #else --cohort "${source.cohort}" --type ${source.format.metadataType} #if $source.format.metadataType == "genomicMatrix" or $source.format.metadataType == "clinicalMatrix": #if $source.format.isCustom.dataSubType == "custom" #if $source.format.isCustom.customSubType --dataSubType "${source.format.isCustom.customSubType}" #end if #else --dataSubType "${source.format.isCustom.dataSubType}" #end if #end if #if $source.label --label "${source.label}" #else --label "${xenaInputData.name}" #end if #end if #if $colNormalization: --colNormalization 1 #end if </command> <inputs> <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> <conditional name="source"> <param type="select" name="metadataSource" label="Metadata entry"> <option value="entry">Enter your own</option> <option value="json">Specify json metadata file</option> </param> <when value="json"> <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/> </when> <when value="entry"> <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> <conditional name="format"> <param type="select" name="metadataType" label="File Format"> <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option> <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option> <option value="mutationVector">Mutation By Position</option> </param> <when value="genomicMatrix"> <conditional name="isCustom"> <param type="select" name="dataSubType" label="Type of data"> <option value="custom">Enter your own</option> <option value="phenotype">phenotype</option> <option value="copy number">copy number</option> <option value="DNA methylation">DNA methylation</option> <option value="exon expression">exon expression</option> <option value="gene expression">gene expression</option> <option value="gene expression RNAseq">gene expression RNAseq</option> <option value="gene expression Array">gene expression Array</option> <option value="mRNA expression">mRNA expression</option> <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> <option value="protein expression RPPA">protein expression RPPA</option> <option value="PARADIGM pathway activity">PARADIGM pathway activity</option> </param> <when value="custom"> <param type="text" name="customSubType" label="Type of data" optional="true"/> </when> <when value="phenotype"/> <when value="copy number"/> <when value="DNA methylation"/> <when value="exon expression"/> <when value="gene expression"/> <when value="gene expression RNAseq"/> <when value="gene expression Array"/> <when value="mRNA expression"/> <when value="somatic mutation (SNP and small INDELs)"/> <when value="somatic mutation (gene level)"/> <when value="protein expression RPPA"/> <when value="PARADIGM pathway activity"/> </conditional> </when> <when value="clinicalMatrix"> <conditional name="isCustom"> <param type="select" name="dataSubType" label="Type of data"> <option value="custom">Enter your own</option> <option value="phenotype">phenotype</option> <option value="copy number">copy number</option> <option value="DNA methylation">DNA methylation</option> <option value="exon expression">exon expression</option> <option value="gene expression">gene expression</option> <option value="gene expression RNAseq">gene expression RNAseq</option> <option value="gene expression Array">gene expression Array</option> <option value="mRNA expression">mRNA expression</option> <option value="somatic mutation (SNP and small INDELs)">somatic mutation (SNP and small INDELs)</option> <option value="somatic mutation (gene level)">somatic mutation (gene level)</option> <option value="protein expression RPPA">protein expression RPPA</option> <option value="PARADIGM pathway activity">PARADIGM pathway activity</option> </param> <when value="custom"> <param type="text" name="customSubType" label="Type of data" optional="true"/> </when> <when value="phenotype"/> <when value="copy number"/> <when value="DNA methylation"/> <when value="exon expression"/> <when value="gene expression"/> <when value="gene expression RNAseq"/> <when value="gene expression Array"/> <when value="mRNA expression"/> <when value="somatic mutation (SNP and small INDELs)"/> <when value="somatic mutation (gene level)"/> <when value="protein expression RPPA"/> <when value="PARADIGM pathway activity"/> </conditional> </when> <when value="mutationVector"/> </conditional> <param type="text" name="label" label="Display Name (Optional)" optional="true"/> </when> </conditional> <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> </inputs> <outputs> <data format="txt" name="outfile"/> </outputs> <help> To Appear, soon... </help> </tool>