<tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
    <description>
        Human RNA virus genotyping pipeline
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
    </requirements>
    <version_command>echo "@TOOL_VERSION@"</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
          #if str( $fastq_input.fastq_input_selector ) == "paired":
            #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
              #set unzipped = False
              #set reads1 = $fastq_input.reads1.name + '_R1.fastq.gz'
            #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
              #set unzipped = True
              #set reads1 = $fastq_input.reads1.name + '_R1.fastq'
            #end if
            ln -s '$fastq_input.reads1' '$reads1' &&
            #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
              #set unzipped = False
              #set reads2 = $fastq_input.reads2.name + '_R2.fastq.gz'
            #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
              #set unzipped = True
              #set reads2 = $fastq_input.reads2.name + '_R2.fastq'
            #end if
            ln -s '$fastq_input.reads2' '$reads2' &&
          #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
            #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
              #set unzipped = False
              #set reads1 = $fastq_input.pair.name + '_R1.fastq.gz'
            #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
              #set unzipped = True
              #set reads1 = $fastq_input.pair.name + '_R1.fastq'
            #end if
            ln -s '$fastq_input.pair.forward' '$reads1' &&
            #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
              #set unzipped = False
              #set reads2 = $fastq_input.pair.name + '_R2.fastq.gz'
            #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
              #set unzipped = True
              #set reads2 = $fastq_input.pair.name + '_R2.fastq'
            #end if
            ln -s '$fastq_input.pair.reverse' '$reads2' &&
          #end if
          
          mkdir 'outdir' &&
          
          micall
            --threads \${GALAXY_SLOTS:-1}
            --keep
            #if $unzipped:
              --unzipped
            #end if
            --readlen ${readlen}
            '${reads1}'
            '${reads2}'
            #if str( $projects_file_source.projects_file_source_selector ) == "tool_data_table":
              --projects '${projects_file_source.projects_file.fields.path}'
            #elif str( $projects_file_source.projects_file_source_selector ) == 'history':
              --projects '${projects_file_source.projects_file}'
            #end if
            --outdir 'outdir'
        ]]>
    </command>
    <inputs>
        <conditional name="fastq_input">
            <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" >
                <option selected="true" value="paired">Paired</option>
                <option value="paired_collection">Paired Collection</option>
            </param>
            <when value="paired">
                <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/>
                <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/>
            </when>
            <when value="paired_collection">
                <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
            </when>
        </conditional>
        <conditional name="projects_file_source">
            <param name="projects_file_source_selector" type="select"
                   label="Select a projects file from your history or use one from a tool data table?">
                <option value="none" selected="true">No projects file</option>
                <option value="tool_data_table">Projects file from tool data table</option>
                <option value="history">Projects file from history</option>
            </param>
            <when value="none"/>
            <when value="tool_data_table">
                <param name="projects_file" type="select" format="json" label="MiCall-Lite Projects File">
                    <options from_data_table="micall_lite_projects_files">
                        <validator type="no_options" message="No MiCall-Lite projects files are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="projects_file" type="data" format="json" label="MiCall-Lite Projects File" help=""/>
            </when>
        </conditional>
        <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
    </inputs>
    <outputs>
        <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
        <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
        <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" />
        <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
        <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
    </outputs>
    <tests>
        <test>
            <conditional name="projects_file_source" >
                <param name="projects_file_source_selector" value="none" />
            </conditional>
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired"/>
                <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
                <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
            </conditional>
            <param name="readlen" value="51" />
            <output name="align" value="1234A-V3LOOP.align.csv" />
            <output name="amino" value="1234A-V3LOOP.amino.csv" />
            <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
            <output name="insert" value="1234A-V3LOOP.insert.csv" />
            <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
        </test>
        <test>
            <conditional name="projects_file_source" >
                <param name="projects_file_source_selector" value="none" />
            </conditional>
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired"/>
                <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
                <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
            </conditional>
            <param name="readlen" value="51" />
            <output name="align" value="1234A-V3LOOP.align.csv" />
            <output name="amino" value="1234A-V3LOOP.amino.csv" />
            <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
            <output name="insert" value="1234A-V3LOOP.insert.csv" />
            <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
        </test>
        <test>
            <conditional name="projects_file_source" >
                <param name="projects_file_source_selector" value="none" />
            </conditional>
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired_collection" />
                <param name="pair" >
                    <collection type="paired">
                        <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
                        <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
                    </collection>
                </param>
            </conditional>
            <param name="readlen" value="51" />
            <output name="align" value="1234A-V3LOOP.align.csv" />
            <output name="amino" value="1234A-V3LOOP.amino.csv" />
            <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
            <output name="insert" value="1234A-V3LOOP.insert.csv" />
            <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
        </test>
        <test>
            <conditional name="projects_file_source" >
                <param name="projects_file_source_selector" value="none" />
            </conditional>
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired_collection" />
                <param name="pair" >
                    <collection type="paired">
                        <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
                        <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
                    </collection>
                </param>
            </conditional>
            <param name="readlen" value="51" />
            <output name="align" value="1234A-V3LOOP.align.csv" />
            <output name="amino" value="1234A-V3LOOP.amino.csv" />
            <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
            <output name="insert" value="1234A-V3LOOP.insert.csv" />
            <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <expand macro="citations" />
</tool>