<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Amend an already loaded GEMINI database.</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">amend</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        cp "${ infile }" "${ outfile }" &&

        gemini @BINARY@
        $clear
        --sample "${ ped }"

        "${ outfile }"
]]>
    </command>
    <inputs>

        <expand macro="infile" />
        <param name="ped" type="data" format="tabular" optional="True" label="Additional sample information file in PED+ format" help="(--sample)" />
        <param argument="--clear" type="boolean" truevalue="--clear" falsevalue="" checked="False" label="Set all values to None before loading" help="Makes it possible to delete values. Otherwise the old ones are kept"/>

    </inputs>
    <outputs>
        <data name="outfile" format="gemini.sqlite" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
            <param name="ped" value="gemini_amend_input.ped" ftype="tabular" />
            <output name="outfile" file="gemini_amend_result.db" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Gemini amend adds information about the samples via PED file.

If you have a sample table in a Gemini db that looks like this::

 sample_id   family_id   name      paternal_id   maternal_id   sex   phenotype   hair_color   
 1           1           M10475    0             0             1     1           brown        
 2           1           M10478    M10475        M10500        2     2           blonde       
 3           1           M10500    0             0             2     2           purple       

and you want the change the haircolor of sample 3. And also add some information about the preferred hobbies of some samples.

You could specify the following PED file. ::

 #family_id  name    paternal_id  maternal_id  sex  phenotype  hair_color  hobby
 1           M10475  None         None         1    1          brown       fishing
 1           M10478  M10475       M10500       2    2          red         biking
 1           M10500  None         None         2    2          purple 

this results in::

 sample_id   family_id   name      paternal_id   maternal_id   sex   phenotype   hair_color   hobby     
 1           1           M10475    0             0             1     1           brown        fishing   
 2           1           M10478    M10475        M10500        2     2           red          biking    
 3           1           M10500    0             0             2     2           purple       .         

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