<tool id="collection_column_join" name="Column join" version="0.0.3">
    <description>on multiple datasets</description>
    <requirements>
        <requirement type="package" version="8.25">coreutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if 'output_shell_script' in str( $include_outputs ).split( "," ):
            cp '${collection_column_join_script}' '${script_output}' &&
        #end if
        sh '${collection_column_join_script}'
    ]]>
    </command>
    <configfiles>
        <configfile name="collection_column_join_script"><![CDATA[
#!/bin/sh
touch header0.tmp &&
touch output0.tmp &&
#set $delimiter = '\t'
#set $left_identifier_column = $identifier_column
#set $tail_offset = int( str( $has_header ) ) + 1
#for $i, $tabular_item in enumerate( $input_tabular ):
    #if $old_col_in_header:
        #if $has_header:
            head -n ${has_header} "${tabular_item}" | awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}_%s", arr[i] ); ctr++ } }; printf( "\n" ); }' > input_header.tmp &&
            tail -n +${tail_offset} "${tabular_item}" | LC_ALL=C sort -t "${delimiter}" -k $identifier_column > input_file.tmp &&
        #else:
            awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}_%s", i ); ctr++ } }; exit }' "${tabular_item}" > input_header.tmp &&
            LC_ALL=C sort -t "${delimiter}" -k $identifier_column "${tabular_item}" > input_file.tmp &&
        #end if
    #else:
        #if $has_header:
            head -n ${has_header} "${tabular_item}" | awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}" ); ctr++ } }; printf( "\n" ); }' > input_header.tmp &&
            tail -n +${tail_offset} "${tabular_item}" | LC_ALL=C sort -t "${delimiter}" -k $identifier_column > input_file.tmp &&
        #else:
            awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}"); ctr++ } }; exit }' "${tabular_item}" > input_header.tmp &&
            LC_ALL=C sort -t "${delimiter}" -k $identifier_column "${tabular_item}" > input_file.tmp &&
        #end if
    #end if
    #if $i == 0:
        mv input_file.tmp output${ ( $i + 1 ) % 2 }.tmp &&
        #if $has_header:
            awk '{ printf \$${identifier_column}; exit }' "${tabular_item}" > header${ $i % 2 }.tmp &&
        #else:
            echo "#KEY" > header${ $i % 2 }.tmp &&
        #end if
    #else:
        LC_ALL=C join -o auto -a 1 -a 2 -1 ${left_identifier_column} -2 ${identifier_column} -t "${delimiter}" -e "${fill_char}" output${ $i % 2 }.tmp input_file.tmp  > output${ ( $i + 1 ) % 2 }.tmp &&
        #set $left_identifier_column = 1
    #end if
    paste -d "${delimiter}" header${ $i % 2 }.tmp input_header.tmp > header${ ( $i + 1 ) % 2 }.tmp &&
#end for
cat header${ ( $i + 1 ) % 2 }.tmp output${ ( $i + 1 ) % 2 }.tmp > "${tabular_output}"
    ]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_tabular" type="data" format="tabular" multiple="True" optional="False" label="Tabular files"/>
        <!-- <param name="identifier_column" type="data_column" data_ref="input_tabular" value="0" min="0" optional="False" label="Identifier column"/> -->
        <param name="identifier_column" type="integer" value="1" min="0" optional="False" label="Identifier column" help="The column that will be used to join the input datasets"/>
        <param name="has_header" type="integer" value="0" min="0" optional="False" label="Number of header lines in each input file" help="If this is set to 0, a header line will be added containing column names as follows: the identifier column will be named #KEY and the other columns are named by the input dataset names/columns. If you have one or more header lines in your input, set this to the number of header lines."/>
        <param name="old_col_in_header" type="boolean" checked="true" label="Add column name to header" help="Disable if you want column headers to only be composed of the input file names, for example, if you want headers like file1 and not file1_column1, see Help section below. Default: Yes"/>
        <param name="fill_char" type="text" value="." optional="False" label="Fill character" help="a placeholder for empty cells"/>
        <param name="include_outputs" type="select" multiple="True" label="Additional datasets to create">
            <option value="output_shell_script" selected="false">Shell script</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="tabular_output"/>
        <data format="txt" name="script_output">
            <filter>include_outputs and "output_shell_script" in include_outputs</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_tabular" value="in_1.tabular,in_2.tabular,in_3.tabular" ftype="tabular"/>
            <param name="identifier_column" value="1"/>
            <param name="has_header" value="1"/>
            <param name="old_col_in_header" value="true"/>
            <param name="fill_char" value="."/>
            <param name="include_outputs" />
            <output name="tabular_output" file="out_1.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input_tabular" value="in_1_headerless.tabular,in_2_headerless.tabular,in_3_headerless.tabular" ftype="tabular"/>
            <param name="identifier_column" value="1"/>
            <param name="has_header" value="0"/>
            <param name="old_col_in_header" value="true"/>
            <param name="fill_char" value="."/>
            <param name="include_outputs" />
            <output name="tabular_output" file="out_2.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input_tabular" value="in_1.tabular,in_2.tabular,in_3.tabular" ftype="tabular"/>
            <param name="identifier_column" value="1"/>
            <param name="has_header" value="1"/>
            <param name="old_col_in_header" value="false"/>
            <param name="fill_char" value="."/>
            <param name="include_outputs" />
            <output name="tabular_output" file="out_3.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input_tabular" value="in_1_headerless.tabular,in_2_headerless.tabular,in_3_headerless.tabular" ftype="tabular"/>
            <param name="identifier_column" value="1"/>
            <param name="has_header" value="0"/>
            <param name="old_col_in_header" value="false"/>
            <param name="fill_char" value="."/>
            <param name="include_outputs" />
            <output name="tabular_output" file="out_4.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
        <![CDATA[
Joins lists of tabular datasets together on a field.

-----

**Example**

To join three files, with headers, based on the first column:

**First file (in_1)**::

    #KEY    c2  c3  c4
    one     1-1 1-2 1-3
    two     1-4 1-5 1-6
    three   1-7 1-8 1-9


**Second File (in_2)**::

    #KEY    c2  c3  c4
    one     2-1 2-2 2-3
    two     2-4 2-5 2-6
    three   2-7 2-8 2-9

**Third file (in_3)**::

    #KEY    c2  c3  c4
    one     3-3 3-2 3-3
    two     3-4 3-5 3-6
    three   3-7 3-8 3-9


**Joining** the files, using **identifier column of 1** and a **header lines of 1**, will return::

    #KEY    in_1_c2 in_1_c3 in_1_c4 in_2_c2 in_2_c3 in_2_c4 in_3_c2 in_3_c3 in_3_c4
    one     1-1              1-2            1-3             2-1              2-2             2-3             3-3             3-2             3-3
    three   1-7              1-8            1-9             2-7              2-8             2-9             3-7             3-8             3-9
    two     1-4              1-5            1-6             2-4              2-5             2-6             3-4             3-5             3-6


**Joining** the files, using **identifier column of 1** and a **header lines of 1**, but disabling **Add column name to header**, will return::

    #KEY    in_1 in_1 in_1 in_2 in_2 in_2 in_3 in_3 in_3
    one     1-1              1-2            1-3             2-1              2-2             2-3             3-3             3-2             3-3
    three   1-7              1-8            1-9             2-7              2-8             2-9             3-7             3-8             3-9
    two     1-4              1-5            1-6             2-4              2-5             2-6             3-4             3-5             3-6

        ]]>
    </help>
    <citations>
    </citations>
</tool>