Mercurial > repos > melissacline > ucsc_xena_platform
annotate xena_import.xml @ 29:fc6f93710384
Fixing a merge issue
| author | melissacline |
|---|---|
| date | Mon, 13 Jul 2015 14:35:34 -0700 |
| parents | d57b5b3af15c |
| children | d8dc482ef970 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="xenaImport" description="Import into XENA from Galaxy" name="XENA Import" version="0.0.1"> |
| 2 <description>Import from Galaxy into the Xena VM</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0">installXena</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 xena_import.py ${xenaInputData} $outfile | |
| 8 #if $source.metadataSource == "json" | |
| 9 --json ${source.xenaMetadata} | |
| 10 #else | |
| 11 --cohort "${source.cohort}" --type ${source.format.metadataType} | |
| 12 #if $source.format.metadataType == "genomicMatrix" or $source.format.metadataType == "clinicalMatrix": | |
| 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 | |
| 20 #end if | |
| 21 #if $source.label | |
| 22 --label "${source.label}" | |
| 23 #else | |
| 24 --label "${xenaInputData.name}" | |
| 25 #end if | |
| 26 #end if | |
|
2
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
27 #if $colNormalization: |
|
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
28 --colNormalization 1 |
|
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
29 #end if |
| 0 | 30 </command> |
| 31 <inputs> | |
| 32 <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/> | |
| 33 <conditional name="source"> | |
| 34 <param type="select" name="metadataSource" label="Metadata entry"> | |
|
4
1707e82d55bc
Tweaking the parameter labels for the xena import tool
melissacline
parents:
2
diff
changeset
|
35 <option value="entry">Enter your own</option> |
| 0 | 36 <option value="json">Specify json metadata file</option> |
| 37 </param> | |
| 38 <when value="json"> | |
| 39 <param format="data" type="data" name="xenaMetadata" label="Metadata file" optional="false"/> | |
| 40 </when> | |
| 41 <when value="entry"> | |
| 42 <param format="str" type="text" name="cohort" label="Cohort" optional="false"/> | |
| 43 <conditional name="format"> | |
| 44 <param type="select" name="metadataType" label="File Format"> | |
|
4
1707e82d55bc
Tweaking the parameter labels for the xena import tool
melissacline
parents:
2
diff
changeset
|
45 <option value="genomicMatrix">Rows (Identifiers) by Columns (Samples) (often genomic data)</option> |
|
1707e82d55bc
Tweaking the parameter labels for the xena import tool
melissacline
parents:
2
diff
changeset
|
46 <option value="clinicalMatrix">Rows (Samples) by Columns (Identifiers) (often clinical data)</option> |
| 0 | 47 <option value="mutationVector">Mutation By Position</option> |
| 48 </param> | |
| 49 <when value="genomicMatrix"> | |
| 50 <conditional name="isCustom"> | |
| 51 <param type="select" name="dataSubType" label="Type of data"> | |
| 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> | |
|
5
c5b71ce5f7b1
Tweaking the xena import options - for a second time (grrr)
melissacline
parents:
2
diff
changeset
|
60 <option value="mRNA expression">mRNA expression</option> |
| 0 | 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"/> | |
|
4
1707e82d55bc
Tweaking the parameter labels for the xena import tool
melissacline
parents:
2
diff
changeset
|
76 <when value="mRNA expression"/> |
| 0 | 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> | |
|
4
1707e82d55bc
Tweaking the parameter labels for the xena import tool
melissacline
parents:
2
diff
changeset
|
94 <option value="mRNA expression">mRNA expression</option> |
| 0 | 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"/> | |
|
4
1707e82d55bc
Tweaking the parameter labels for the xena import tool
melissacline
parents:
2
diff
changeset
|
110 <when value="mRNA expression"/> |
| 0 | 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> | |
| 121 </conditional> | |
|
2
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
122 <param type="boolean" name="colNormalization" label="Apply Column Normalization" checked="false"/> |
| 0 | 123 </inputs> |
| 124 <outputs> | |
| 125 <data format="txt" name="outfile"/> | |
| 126 </outputs> | |
| 127 <help> | |
|
8
d57b5b3af15c
Minor update to ensure that xena_import correctly has the 'enter your own' metadata option appear first
melissacline
parents:
6
diff
changeset
|
128 To Appear, soon... |
| 0 | 129 </help> |
| 130 </tool> |