<tool id="confindr" name="ConFindr" version="@VERSION@+galaxy0">
    <description>
        Intra-species bacterial contamination detection
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[
        mkdir input &&
        mkdir databases &&
        #if str( $reads_input.reads_input_selector ) == "paired"
          ln -s '$reads_input.reads_1' 'input/reads_R1.fastq' &&
          ln -s '$reads_input.reads_2' 'input/reads_R2.fastq' &&
        #end if
        #if str( $reads_input.reads_input_selector ) == "paired_collection"
          ln -s '$reads_input.reads.forward' 'input/reads_R1.fastq' &&
          ln -s '$reads_input.reads.reverse' 'input/reads_R2.fastq' &&
        #end if
        
        confindr.py 
          --threads \${GALAXY_SLOTS:-1}
          --databases 'databases'
          --input_directory 'input'
          --output_name 'output'

    ]]></command>

    <inputs>
        <conditional name="reads_input">
            <param name="reads_input_selector" type="select" label="Paired-end reads or paired collection" help="Select between paired and paired collection">
                <option value="paired">Paired</option>
                <option value="paired_collection">Paired Collection</option>
            </param>
            <when value="paired">
                <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
                <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
            </when>
            <when value="paired_collection">
                <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="report" format="csv" from_work_dir="output/confindr_report.csv" label="${tool.name} on ${on_string} report file" />
    </outputs>

    <tests>
        

    </tests>

    <help><![CDATA[
**What it does**



**Output**

ConFindr will produce a tab-seperated output file with the following outputs:

+--------------------------------+------------------------------------------------+
|  Column                        | Description                                    |
+================================+================================================+
| Sample                         |                                                |
+--------------------------------+------------------------------------------------+
| Genus                          |                                                |
+--------------------------------+------------------------------------------------+
| ContamStatus                   |                                                |
+--------------------------------+------------------------------------------------+
| PercentContam                  |                                                |
+--------------------------------+------------------------------------------------+
| PercentContamStandardDeviation |                                                |
+--------------------------------+------------------------------------------------+
| BasesExamined                  |                                                |
+--------------------------------+------------------------------------------------+
| DatabaseDownloadDate           |                                                |
+--------------------------------+------------------------------------------------+

**Example Output**

::
Sample,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamStandardDeviation,BasesExamined,DatabaseDownloadDate


    ]]></help>

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