view secimtools/summarize_flags.xml @ 0:b54326490b4d draft

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<tool id="secimtools_summarize_flags" name="Summarize Flags in a Flag File" version="@WRAPPER_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
summarize_flags.py
--flags $flags
--ID $uniqID
--outSummary $summaryFlags
    ]]></command>
    <inputs>
        <param name="flags" type="data" format="tabular" label="Flag File"
               help="Input flagged dataset containing the flag value for each feature."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID"
               help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
    </inputs>
    <outputs>
        <data name="summaryFlags" format="tabular" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="flags"   value="ST000006_lasso_enet_var_select_flags.tsv"/>
            <param name="uniqID"  value="Retention_Index" />
            <output name="summaryFlags" file="ST000006_summarize_flags_outSummary.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

Summary of the Flags

This tool takes a wide format flag file and summarizes the information about the flags.
The flag summary includes, for each feature:
(i) the sum of the flags,
(ii) the mean of the flags,
(iii) an indicator if at least one of the original flags had a value of 1 and
(iv) a second indicator if all of the original flags had a value of 1.

--------------------------------------------------------------------------------

**Input**

    - One input dataset is required.

@FLAGS@

@UNIQID@

--------------------------------------------------------------------------------

**Output**

This tool will output a TSV file containing all original input flag data with four additional columns containing the flag summaries.

The four additional columns are:

(i) a column with the sum of the flags,
(ii) a column with the flag means, and
(iii) a flag indicator column if at least one of the original flags had a value of 1
(iv) a second flag indicator column if all of the original flags had a value of 1


    ]]></help>
    <expand macro="citations"/>
</tool>