<tool profile="16.07" id="mothur_make_sra" name="Make.sra" version="@WRAPPER_VERSION@.0">
    <description>creates the necessary files for a NCBI submission</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$project' project.dat &&
ln -s '$sff' sff.dat &&
ln -s '$oligos' oligos.dat &&
ln -s '$mimark' mimark.dat &&
ln -s '$fastq' fastq.dat &&

echo 'make.sra(
    project=project.dat,
    sff=sff.dat,
    oligos=oligos.dat,
    mimark=mimark.dat,
    #if $fastq:
        fastq=fastq.dat,
    #end if
    bdiffs=$bdiffs,
    pdiffs=$pdiffs,
    tdiffs=$tdiffs,
    ldiffs=$ldiffs,
    sdiffs=$sdiffs,
    checkorient=$checkorient,
    orientation=$orientation,
    platform=$platform,
    instrument=$instrument,
    libstrategy=$libstrategy,
    libselection=$libselection,
    libsource=$libsource,
    datatype=$datatype,
    trim=$trim,
    includescrap=$includescrap
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="project" type="data" format="tabular" label="Project file"/>
        <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
        <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>
        <param name="mimark" type="data" format="txt" label="mimarks file - you can create the template for this file using the get.mimarkspackage command"/>
        <param name="fastq" type="data" optional="true" format="fastq" label="fastq - provide the original fastq file"/>
        <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
        <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
        <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/>
        <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/>
        <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/>
        <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - will check for the reverse compliment of the barcode or primer in the sequence. The default is false."/>
        <param name="orientation" type="select" label="orientation - specify the sequence orientation">
            <option value="forward" selected="true">forward</option>
            <option value="reverse">reverse</option>
        </param>
        <param name="platform" type="select" label="platform - specify platform you are using" help="This is a controlled vocabulary section in the XML file that will be generated">
            <option value="_LS454" selected="true">454 (_LS454)</option>
            <option value="ILLUMINA">Illumina (ILLUMINA)</option>
            <option value="ION_TORRENT">Ion Torrent (ION_TORRENT)</option>
            <option value="PACBIO_SMRT">PacBio (PACBIO_SMRT)</option>
        </param>
        <param name="instrument" type="select" label="instrument - specify instrument" help="This is a controlled vocabulary section in the XML file that will be generated">
            <option value="454_GS" selected="true">454_GS</option>
            <option value="454_GS_20">454_GS_20</option>
            <option value="454_GS_FLX">454_GS_FLX</option>
            <option value="454_GS_FLX_Titanium">454_GS_FLX_Titanium</option>
            <option value="454_GS_Junior">454_GS_Junior</option>
            <option value="Illumina_Genome_Analyzer">Illumina_Genome_Analyzer</option>
            <option value="Illumina_Genome_Analyzer_II">Illumina_Genome_Analyzer_II</option>
            <option value="Illumina_Genome_Analyzer_IIx">Illumina_Genome_Analyzer_IIx</option>
            <option value="Illumina_HiSeq_2000">Illumina_HiSeq_2000</option>
            <option value="Illumina_HiSeq_1000">Illumina_HiSeq_1000</option>
            <option value="Illumina_MiSeq">Illumina_MiSeq</option>
            <option value="PacBio_RS">PacBio_RS</option>
            <option value="Ion_Torrent_PGM">Ion_Torrent_PGM</option>
            <option value="unspecified">unspecified</option>
        </param>
        <param name="libstrategy" type="select" label="libstrategy - specify library strategy" help="This is a controlled vocabulary section in the XML file that will be generated">
            <option value="AMPLICON" selected="true">AMPLICON</option>
            <option value="WGA">WGA</option>
            <option value="WGS">WGS</option>
            <option value="RNA-Seq">RNA-Seq</option>
            <option value="miRNA-Se">miRNA-Se</option>
            <option value="WCS">WCS</option>
            <option value="CLONE">CLONE</option>
            <option value="POOLCLONE">POOLCLONE</option>
            <option value="CLONEEND">CLONEEND</option>
            <option value="FINISHING">FINISHING</option>
            <option value="ChIP-Seq">ChIP-Seq</option>
            <option value="MNase-Seq">MNase-Seq</option>
            <option value="DNase-Hypersensitivity">DNase-Hypersensitivity</option>
            <option value="Bisulfite-Seq">Bisulfite-Seq</option>
            <option value="Tn-Seq">Tn-Seq</option>
            <option value="EST">EST</option>
            <option value="FL-cDNA">FL-cDNA</option>
            <option value="CTS">CTS</option>
            <option value="MRE-Seq">MRE-Seq</option>
            <option value="MeDIP-Seq">MeDIP-Seq</option>
            <option value="MBD-Seq">MBD-Seq</option>
            <option value="OTHER">OTHER</option>
        </param>
        <param name="libsource" type="select" label="libsource - specify library source" help="This is a controlled vocabulary section in the XML file that will be generated">
            <option value="METAGENOMIC" selected="true">METAGENOMIC</option>
            <option value="GENOMIC">GENOMIC</option>
            <option value="TRANSCRIPTOMIC">TRANSCRIPTOMIC</option>
            <option value="METATRANSCRIPTOMIC">METATRANSCRIPTOMIC</option>
            <option value="SYNTHETIC">SYNTHETIC</option>
            <option value="VIRAL_RNA">VIRAL_RNA</option>
            <option value="OTHER">OTHER</option>
        </param>
        <param name="libselection" type="select" label="libselection - specify library selection" help="This is a controlled vocabulary section in the XML file that will be generated">
            <option value="PCR" selected="true">PCR</option>
            <option value="RANDOM">RANDOM</option>
            <option value="RANDOM_PCR">RANDOM_PCR</option>
            <option value="RT-PCR">RT-PCR</option>
            <option value="HMPR">HMPR</option>
            <option value="MF">MF</option>
            <option value="CF-S">CF-S</option>
            <option value="CF-H">CF-H</option>
            <option value="CF-T">CF-T</option>
            <option value="CF-M">CF-M</option>
            <option value="MDA">MDA</option>
            <option value="MSLL">MSLL</option>
            <option value="cDNA">cDNA</option>
            <option value="ChIP">ChIP</option>
            <option value="MNase">MNase</option>
            <option value="Hybrid_Selection">Hybrid_Selection</option>
            <option value="Reduced_Representation">Reduced_Representation</option>
            <option value="Restriction_Digest">Restriction_Digest</option>
            <option value="5-methylcytidine_antibody">5-methylcytidine_antibody</option>
            <option value="MBD2_protein_methyl-CpG_binding_domain">MBD2_protein_methyl-CpG_binding_domain</option>
            <option value="CAGE">CAGE</option>
            <option value="RACE">RACE</option>
            <option value="size_fractionation">size_fractionation</option>
            <option value="Padlock_probes_capture_method">Padlock_probes_capture_method</option>
            <option value="other">other</option>
        </param>
        <param name="datatype" type="select" label="datatype - specify datatype" help="This is a controlled vocabulary section in the XML file that will be generated">
            <option value="METAGENOME" selected="true">METAGENOME</option>
            <option value="GENOME_SEQUENCING">GENOME_SEQUENCING</option>
            <option value="METAGENOMIC_ASSEMBLY">METAGENOMIC_ASSEMBLY</option>
            <option value="ASSEMBLY">ASSEMBLY</option>
            <option value="TRANSCRIPTOME">TRANSCRIPTOME</option>
            <option value="PROTEOMIC">PROTEOMIC</option>
            <option value="MAP">MAP</option>
            <option value="CLONE_ENDS">CLONE_ENDS</option>
            <option value="TARGETED_LOCI">TARGETED_LOCI</option>
            <option value="RANDOM_SURVEY">RANDOM_SURVEY</option>
            <option value="EXOME">EXOME</option>
            <option value="VARIATION">VARIATION</option>
            <option value="EPIGENOMICS">EPIGENOMICS</option>
            <option value="PHENOTYPE">PHENOTYPE</option>
            <option value="GENOTYPE">GENOTYPE</option>
            <option value="OTHER">OTHER</option>
        </param>
        <param name="trim" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Trim sequences and quality scores?" help="will trim to the clipQualLeft and clipQualRight values in sff file"/>
        <param name="includescrap" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Include scrapped sequences in your submission?"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
        <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>
        <data name="flow_out" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flow"/>
        <data name="scrap_sff" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap sff"/>
        <data name="submission_xml" format="xml" from_work_dir="submission.xml" label="${tool.name} on ${on_string}: submission.xml"/>
    </outputs>
    <tests>
        <test><!-- test with defauts -->
            <param name="project" value="makesra.project" ftype="tabular"/>
            <param name="sff" value="Fasting_Example1.sff" ftype="sff"/>
            <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
            <param name="mimark" value="biosample.tsv" ftype="tabular"/>
            <output name="fasta_out" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
            <output name="qual_out" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual"/>
            <output name="flow_out" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
            <output name="scrap_sff" ftype="sff">
                <assert_contents>
                    <has_text text="FLP3FBN01ELBSX"/>
                </assert_contents>
            </output>
            <output name="submission_xml" ftype="xml">
                <assert_contents>
                    <has_text text="Submission"/>
                    <has_text text="Attribute"/>
                    <has_text text="BioProject"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The make.sra_ creates the necessary files for a NCBI submission.

.. _make.sra: https://www.mothur.org/wiki/Make.sra

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