view cluster.tools/format.raw.TCGA.RNASeq.data.xml @ 3:563832f48c08 draft

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<tool id="format_raw_TCGA_RNASeq_data" name="Format Raw TCGA RNASeq Data" force_history_refresh="True">
    <command interpreter="python">format.raw.TCGA.RNASeq.data.py
-d $dataset
-l {$log_transform}
-f ${filter_low_variant}
-o ${output}

</command>
    <inputs>
    	<param name="dataset" type="data" format='tabular' label="Raw TCGA RNASeq Data"/>
        <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))">
          <option value="yes" selected='true' >Yes</option>
          <option value="no">No</option>
        </param>
        <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)">
          <option value="yes" selected='true' >Yes</option>
          <option value="no">No</option>
        </param>

    </inputs>
    <outputs>
        <data format="tabular" name="output" label="Formatted RNASeq Data"/>
    </outputs>
<help>
.. class:: infomark
     
**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

**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

**OUTPUT:**  A new tab-delimited file containing the log-transformed RNASeq data

</help>
</tool>