<tool id="cami_amber_add" name="CAMI AMBER add length column" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Create gold standard file for CAMI AMBER</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[

        ln -s '${gold_standard_file}' '$gold_standard_file.element_identifier' &&
        ln -s '${fasta_file}' '$fasta_file.element_identifier' &&

        add_length_column.py 
        -g '$gold_standard_file.element_identifier'
        -f '$fasta_file.element_identifier'
        > gold_standard_file.tsv
    ]]>
    </command>
    <inputs>
        <param argument="--gold_standard_file" type="data" format="tabular"
            label="Input gold standard file here"
            help="Input a binning file in biobox format to generate a biobox format file with the extra column 'Length' which is needed for AMBER. Every other biobox format can be used for this as well!" />
        <param argument="--fasta_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz"
            label="Input fasta/fastq file here"
            help="Input the file which match to the gold standard file" />
    </inputs>
    <outputs>
        <data name="file" format="tabular" from_work_dir="gold_standard_file.tsv" label="${tool.name}: Gold standard file" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="gold_standard_file" value="test_add.tsv" ftype="tabular" />
            <param name="fasta_file" value="test_add.fasta.gz" ftype="fasta.gz" />
            <output name="file" >
                <assert_contents>
                    <has_size value="124000" delta="3000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
    <![CDATA[
        .. class:: infomark

        **What it does**

        This tool can create the gold standard file which has to be used for the CAMI AMBER. 

        **Input**

        This tool required 2 inputs:

        - A binning file (biobox format)

        This file can be created via the convert_to_biobox tool

        .. class:: infomark

        Example(tab separated):

        ::

         #CAMI Format for Binning
         @Version:0.9.0
         @SampleID:CAMI_low
         @@SEQUENCEID	BINID
         RL|S1|C10	Bin_034
         RL|S1|C100	Bin_023
         RL|S1|C1000	Bin_034
         RL|S1|C10000	Bin_019
         RL|S1|C10002	Bin_035
         RL|S1|C10004	Bin_035
         RL|S1|C10008	Bin_034
         RL|S1|C10011	Bin_035
         RL|S1|C10012	Bin_013
         RL|S1|C10014	Bin_035

        - A fasta/fastq file (fasta,fasta.gz,fastq,fastq.gz format)

        This file need the identical sequences which are in the gold standard file to create the finish gold standard file for CAMI AMBER

        **Output**

        As output the tool give you out a file in biobox format with the added column 'Length'. This file then can be used for AMBER as example!


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