<?xml version="1.0"?>
<tool id="cummerbund_to_cuffdiff" name="Extract CuffDiff" version="1.0.1">
    <description>tabular files from a cummeRbund database</description>
    <command interpreter="python"><![CDATA[
        cummerbund_to_tabular.py --file ${input_database} ${' '.join(str($tables).split(','))}
        ]]></command>
    <inputs>
        <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
        <param type="select" name="tables" multiple="True" label="Select tables to output">
            <option name="cds_count" value="--tables cds_count">CDS count tracking</option>
            <option name="cds_diff" value="--tables cds_diff">CDS overloading diffential expression testing</option>
            <option name="cds_exp_diff" value="--tables cds_exp_diff">CDS FPKM differential expression testing</option>
            <option name="cds_fpkm" value="--tables cds_fpkm">CDS FPKM tracking</option>
            <option name="cds_rg" value="--tables cds_rg">CDS read groups</option>
            <option name="gene_exp_diff" value="--tables gene_exp_diff">Gene differential expression testing</option>
            <option name="genes_count" value="--tables genes_count">Gene count tracking</option>
            <option name="genes_fpkm" value="--tables genes_fpkm">Gene FPKM tracking</option>
            <option name="gene_rg" value="--tables gene_rg">Gene read groups</option>
            <option name="isoform_exp_diff" value="--tables isoform_exp_diff">Transcript differential expression testing</option>
            <option name="isoform_count" value="--tables isoform_count">Transcript count tracking</option>
            <option name="isoform_fpkm" value="--tables isoform_fpkm">Transcript FPKM tracking</option>
            <option name="isoform_rg" value="--tables isoform_rg">Transcript read groups</option>
            <option name="promoters_diff" value="--tables promoters_diff">Promoter differential testing</option>
            <option name="read_groups" value="--tables read_groups">Read Groups</option>
            <option name="run_info" value="--tables run_info">Run details</option>
            <option name="splicing_diff" value="--tables splicing_diff">Splicing differential expression testing</option>
            <option name="tss_group_exp" value="--tables tss_group_exp">TSS groups differential expression testing</option>
            <option name="tss_count_tracking" value="--tables tss_count_tracking">TSS count FPKM tracking</option>
            <option name="tss_fpkm" value="--tables tss_fpkm">TSS groups FPKM tracking</option>
            <option name="tss_rg" value="--tables tss_rg">TSS read groups</option>
            <option name="var_model" value="--tables var_model">Model info</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="cds_count_output" from_work_dir="cds_count.tabular" label="${tool.name} on ${on_string}: CDS count tracking">
            <filter>('--tables cds_count' in tables)</filter>
        </data>
        <data format="tabular" name="cds_diff_output" from_work_dir="cds_diff.tabular" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
            <filter>('--tables cds_diff' in tables)</filter>
        </data>
        <data format="tabular" name="cds_exp_diff_output" from_work_dir="cds_exp_diff.tabular" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing">
            <filter>('--tables cds_exp_diff' in tables)</filter>
        </data>
        <data format="tabular" name="cds_fpkm_output" from_work_dir="cds_fpkm.tabular" label="${tool.name} on ${on_string}: CDS FPKM tracking">
            <filter>('--tables cds_fpkm' in tables)</filter>
        </data>
        <data format="tabular" name="cds_rg_output" from_work_dir="cds_rg.tabular" label="${tool.name} on ${on_string}: CDS read groups">
            <filter>('--tables cds_rg' in tables)</filter>
        </data>
        <data format="tabular" name="gene_exp_diff_output" from_work_dir="gene_exp_diff.tabular" label="${tool.name} on ${on_string}: gene differential expression testing">
            <filter>('--tables gene_exp_diff' in tables)</filter>
        </data>
        <data format="tabular" name="genes_count_output" from_work_dir="genes_count.tabular" label="${tool.name} on ${on_string}: gene count tracking">
            <filter>('--tables genes_count' in tables)</filter>
        </data>
        <data format="tabular" name="genes_fpkm_output" from_work_dir="genes_fpkm.tabular" label="${tool.name} on ${on_string}: gene FPKM tracking">
            <filter>('--tables genes_fpkm' in tables)</filter>
        </data>
        <data format="tabular" name="gene_rg_output" from_work_dir="gene_rg.tabular" label="${tool.name} on ${on_string}: gene read groups">
            <filter>('--tables gene_rg' in tables)</filter>
        </data>
        <data format="tabular" name="isoform_exp_diff_output" from_work_dir="isoform_exp_diff.tabular" label="${tool.name} on ${on_string}: transcript differential expression testing">
            <filter>('--tables isoform_exp_diff' in tables)</filter>
        </data>
        <data format="tabular" name="isoform_count_output" from_work_dir="isoform_count.tabular" label="${tool.name} on ${on_string}: transcript count tracking">
            <filter>('--tables isoform_count' in tables)</filter>
        </data>
        <data format="tabular" name="isoform_fpkm_output" from_work_dir="isoform_fpkm.tabular" label="${tool.name} on ${on_string}: transcript FPKM tracking">
            <filter>('--tables isoform_fpkm' in tables)</filter>
        </data>
        <data format="tabular" name="isoform_rg_output" from_work_dir="isoform_rg.tabular" label="${tool.name} on ${on_string}: transcript read groups">
            <filter>('--tables isoform_rg' in tables)</filter>
        </data>
        <data format="tabular" name="promoters_diff_output" from_work_dir="promoters_diff.tabular" label="${tool.name} on ${on_string}: promoter differential testing">
            <filter>('--tables promoters_diff' in tables)</filter>
        </data>
        <data format="tabular" name="read_groups_output" from_work_dir="read_groups.tabular" label="${tool.name} on ${on_string}: Read Groups">
            <filter>('--tables read_groups' in tables)</filter>
        </data>
        <data format="tabular" name="run_info_output" from_work_dir="run_info.tabular" label="${tool.name} on ${on_string}: Run details">
            <filter>('--tables run_info' in tables)</filter>
        </data>
        <data format="tabular" name="splicing_diff_output" from_work_dir="splicing_diff.tabular" label="${tool.name} on ${on_string}: splicing differential expression testing">
            <filter>('--tables splicing_diff' in tables)</filter>
        </data>
        <data format="tabular" name="tss_group_exp_output" from_work_dir="tss_group_exp.tabular" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
            <filter>('--tables tss_group_exp' in tables)</filter>
        </data>
        <data format="tabular" name="tss_count_tracking_output" from_work_dir="tss_count_tracking.tabular" label="${tool.name} on ${on_string}: TSS count FPKM tracking">
            <filter>('--tables tss_count_tracking' in tables)</filter>
        </data>
        <data format="tabular" name="tss_fpkm_output" from_work_dir="tss_fpkm.tabular" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
            <filter>('--tables tss_fpkm' in tables)</filter>
        </data>
        <data format="tabular" name="tss_rg_output" from_work_dir="tss_rg.tabular" label="${tool.name} on ${on_string}: TSS read groups">
            <filter>('--tables tss_rg' in tables)</filter>
        </data>
        <data format="tabular" name="var_model_output" from_work_dir="var_model.tabular" label="${tool.name} on ${on_string}: var_model.info">
            <filter>('--tables var_model' in tables)</filter>
        </data>
    </outputs>
    <citations>
        <citation type="doi">doi:10.1038/nprot.2012.016</citation>
    </citations>
    <help>This tool extracts cuffdiff tabular files from a cummeRbund SQLite database.</help>
    <tests>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables cds_count,--tables cds_diff,--tables cds_exp_diff,--tables cds_fpkm,--tables cds_rg,--tables gene_exp_diff,--tables genes_count,--tables genes_fpkm,--tables gene_rg,--tables isoform_exp_diff,--tables isoform_count,--tables isoform_fpkm,--tables isoform_rg,--tables promoters_diff,--tables read_groups,--tables run_info,--tables splicing_diff,--tables tss_group_exp,--tables tss_count_tracking,--tables tss_fpkm,--tables tss_rg,--tables var_model" />
            <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
            <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
            <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
            <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
            <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
            <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
            <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
            <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
            <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
            <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
            <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
            <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
            <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
            <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
            <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
            <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
            <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
            <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
            <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
            <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
            <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
            <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables cds_count" />
            <output name="cds_count_output" ftype="tabular" file="cds_count.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables cds_diff" />
            <output name="cds_diff_output" ftype="tabular" file="cds_diff.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables cds_exp_diff" />
            <output name="cds_exp_diff_output" ftype="tabular" file="cds_exp_diff.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables cds_fpkm" />
            <output name="cds_fpkm_output" ftype="tabular" file="cds_fpkm.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables cds_rg" />
            <output name="cds_rg_output" ftype="tabular" file="cds_rg.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables gene_exp_diff" />
            <output name="gene_exp_diff_output" ftype="tabular" file="gene_exp_diff.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables genes_count" />
            <output name="genes_count_output" ftype="tabular" file="genes_count.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables genes_fpkm" />
            <output name="genes_fpkm_output" ftype="tabular" file="genes_fpkm.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables gene_rg" />
            <output name="gene_rg_output" ftype="tabular" file="gene_rg.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables isoform_exp_diff" />
            <output name="isoform_exp_diff_output" ftype="tabular" file="isoform_exp_diff.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables isoform_count" />
            <output name="isoform_count_output" ftype="tabular" file="isoform_count.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables isoform_fpkm" />
            <output name="isoform_fpkm_output" ftype="tabular" file="isoform_fpkm.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables isoform_rg" />
            <output name="isoform_rg_output" ftype="tabular" file="isoform_rg.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables promoters_diff" />
            <output name="promoters_diff_output" ftype="tabular" file="promoters_diff.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables read_groups" />
            <output name="read_groups_output" ftype="tabular" file="read_groups.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables run_info" />
            <output name="run_info_output" ftype="tabular" file="run_info.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables splicing_diff" />
            <output name="splicing_diff_output" ftype="tabular" file="splicing_diff.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables tss_group_exp" />
            <output name="tss_group_exp_output" ftype="tabular" file="tss_group_exp.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables tss_count_tracking" />
            <output name="tss_count_tracking_output" ftype="tabular" file="tss_count_tracking.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables tss_fpkm" />
            <output name="tss_fpkm_output" ftype="tabular" file="tss_fpkm.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables tss_rg" />
            <output name="tss_rg_output" ftype="tabular" file="tss_rg.tabular" />
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
            <param name="tables" value="--tables var_model" />
            <output name="var_model_output" ftype="tabular" file="var_model.tabular" />
        </test>
    </tests>
</tool>