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1 <tool id="format_raw_TCGA_RNASeq_data" name="Format Raw TCGA RNASeq Data" force_history_refresh="True">
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2 <command interpreter="python">format.raw.TCGA.RNASeq.data.py
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3 -d $dataset
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4 -l {$log_transform}
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5 -f ${filter_low_variant}
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6 -o ${output}
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7
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8 </command>
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9 <inputs>
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10 <param name="dataset" type="data" format='tabular' label="Raw TCGA RNASeq Data"/>
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11 <param name="log_transform" type='select' display="radio" label="Log-transform data?" help="Specify whether or not to log-transform the data matrix (log(x+1))">
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12 <option value="yes" selected='true' >Yes</option>
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13 <option value="no">No</option>
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14 </param>
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15 <param name="filter_low_variant" type='integer' label="Filter Threshold for Low-variant genes?" value="10" help="Specify threshold for minimum median value for all genes (-1 to use no filter)">
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16 <option value="yes" selected='true' >Yes</option>
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17 <option value="no">No</option>
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18 </param>
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19
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="output" label="Formatted RNASeq Data"/>
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23 </outputs>
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24 <help>
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25 .. class:: infomark
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26
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27 **Format Raw TCGA RNASeq Data** - Tool to convert a raw RNASeq TCGA data file (a file from either Synapse or Firehose) into a the format expected by the Survival Analysis tools
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28
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29 **Log-transform data?** - Specify whether or not to log-transform the data matrix. To avoid numeric underflow, this will use log(x+1), where x is the value of the RNASeq data
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30
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31 **OUTPUT:** A new tab-delimited file containing the log-transformed RNASeq data
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32
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33 </help>
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34 </tool>
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