<tool id="secimtools_merge_flags" name="Merge Flag Files" version="@WRAPPER_VERSION@">
    <description>with the same unique identifiers into a single file.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
merge_flags.py
--input "$input"
--output "$output"
#set names = '" "'.join( [ str( $i.display_name ) for $i in $input ] )
--filename "${names}"
#if $flagUniqID
    --flagUniqID $flagUniqID
#end if
    ]]></command>
    <inputs>
        <param name="input" format="tabular" type="data"  label="Input Flag Files" multiple="true" help="Input your tab-separated flag files. CTRL+CLICK to select multiple files. If not tab separated see TIP below." />
        <param name="flagUniqID" type="text" size="30" value="" label="Unique identifier in the flag files (feature or sample)" help="Name of the column in your flag file that contains unique identifiers."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}: Flags"/>
    </outputs>
    <tests>
        <test>
            <param name="input"      value="ST000006_run_order_regression_flags.tsv,ST000006_lasso_enet_var_select_flags.tsv"/>
            <param name="flagUniqID" value="Retention_Index" />
            <param name="filename"   value="ST000006_run_order_regression_flags ST000006_lasso_enet_var_select_flags" />
            <output name="output"    file="ST000006_merge_flags_output.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool merges two or more flag files together.  The flag files can be either in wide format or in design format.

The merging requirements are:

(1) the number of rows should be the same in all files being merged and
(2) all files should contain the same unique ID column name to merge by.

**Note:** More broadly, the tool can merge non-metabolomics data as long ast he above requirements are met.


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

**Input**

    - Two or more datasets are required.

@WIDE@

**NOTE:** The sample IDs must match the sample IDs in the Design File (below).
Extra columns will automatically be ignored.

@METADATA@

**Unique ID for Flag file (feature ID or sample ID).**

    - Name of the column in your Flag file that contains unique IDs.


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

**Output**

The TSV output contains all columns from the flag files.  The column with the unique row ID will be included once in the output dataset.

**Note:** If the input flag files have the same flag column name in multiple files,  the merged file will have columns from all imputed files.
To distinguish columns obtained from different files, column names will be altered by appending the corresponding file name to the end of the column name.
All non-supported file name characters will be changed to ‘_’.


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