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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/cistrome_beta commit d824634e1b43fd7f2628631d2d4443ca1cd1ecce-dirty

<tool id="beta_basic" name="BETA-basic: Binding and Expression Target Analysis" version="@VERSION@.0">
    <description>Predict the factors (TFs or CRs) direct target genes by combining the binding and expression data</description>
    <macros>
        <import>beta_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
        BETA basic 
        #include source=$common_opts#
        #include source=$genome_opts#
        #include source=$extended_opts#
        #include source=$write_log#
    ]]></command>
    <inputs>
        <expand macro="common_params" />
        <expand macro="genome_params" />
        <expand macro="extended_params" />
    </inputs>
    <outputs>
        <data format="txt" name="log" label="Log of BETA basic"/>
        <data format="pdf" name="functionoutput" label="BETA functional prediction on ${peakfile.name}" from_work_dir="BETA_OUTPUT/NA_function_prediction.pdf"/>
        <data format="tabular" name="uptargetsoutput" label="BETA direct targets prediction on up regulated genes" from_work_dir="BETA_OUTPUT/NA_uptarget.txt"/>
        <data format="tabular" name="downtargetsoutput" label="BETA direct targets prediction on down regulated genes" from_work_dir="BETA_OUTPUT/NA_downtarget.txt"/>
        <data format="bed" name="uptargetpeaks" label="BETA Uptarget associated peaks" from_work_dir="BETA_OUTPUT/NA_uptarget_associate_peaks.bed"/>
        <data format="bed" name="downtargetpeaks" label="BETA Downtarget associated peaks" from_work_dir="BETA_OUTPUT/NA_downtarget_associate_peaks.bed"/>
    </outputs>
    <tests>
        <test>
            <param name='peakfile' value="peaks.bed" ftype="bed" dbkey="hg19"/>
            <param name="distance" value="100000"/>
            <param name="peaknumber" value="10000"/>
            <param name="genomeName" value="hg19"/>
            <param name='exprefile' value="diff_expr.xls" ftype="tabular" dbkey="hg19"/>
            <param name="kind" value="LIM"/>
            <param name="expreinfo" value="2,5,7"/>
            <param name="gname2" value="Refseq"/>
            <param name="diff_fdr" value="1.0"/>
            <param name="diff_amount" value="0.5"/>
            <param name="method" value="score"/>
            <output name="log">
                <assert_contents>
                    <has_text_matching expression="Finished" />
                </assert_contents>
            </output>
            <output name="uptargetsoutput">
                <assert_contents>
                    <has_text_matching expression="chr19\t47990890\t48018515\tNR_038457\t4.*\t-\tNAPA" />
                </assert_contents>
            </output>
            <output name="uptargetpeaks">
                <assert_contents>
                    <has_text_matching expression="chr19\t47950633\t47951639\tNR_038457\tNAPA\t-67379\t0.04\d+" />
                </assert_contents>
            </output>
        </test>
    </tests>
 <help><![CDATA[
** BETA basic **

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

This tool annotates the given intervals and scores with genome
features such as gene body. It's the major module in CEAS package
which is written by Hyunjin Gene Shin, published in Bioinformatics
(pubmed id:19689956).

.. class:: warningmark

**NEED IMPROVEMENT**

-----

**Parameters**

- **PEAKFILE file** contains peaks for the experiment in a bed
    format file. Normally, it's produced by the peak calling tool. It's
    required.
- **EXPREFILE file** contains the differentially expressed genes in a tab 
    delimited text file. It's required.
- **Kind** The kind of your expression file format, LIM for LIMMA standard 
    output with Microarray, CUF for Cuffdiffs standard output with RNA-seq, 
    BSF for BETA specific format, and O for other formats.
- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter.
- **gname2** If this switch is on, gene or transcript IDs in files given 
    through -e will be considered as official gene symbols, DEFAULT=FALSE
- **EXPREINFO** is the columns info of the geneID, up/down status and statistcal
    values column of your expression data,NOTE: use a comma as an connector. 
    for example: 2,5,7 means geneID in the 2nd column, Tscore in 5th column 
    and FDR in 7 column.
- **REFERENCE** is the refgene info file downloaded from UCSC genome browser.
    It is a tab delimited text file with gene annotation with refseq and gene symbol.
    Input this file only if your genome is neither hg19 nor mm9.
    profiling
- **OUTPUT** to specify the output files directory
- **bl** Whether or not to use CTCF boundary file to get the contributed peaks
- **BOUNDARYFILE** is the file with reasonable boundaries if --bl is on and genome
    is neither hg19 nor mm9.
- **NAME** specify the name of the output files.
- **DISTANCE** specify the distance wich peaks within it will be considered.
- **DIFF_FDR** specify the differential genes by the 3rd column in file input
    via -e, genes with less than this value will be considered as the differentially
    changed genes.
- **DIFF_AMOUNT** specify the differential genes the top #(DIFF_AMOUNT) ranked by
    the 3rd column in file input via -e, genes ranked in the top # will be considered
    as the differentially expressed genes.
- **CUTOFF** specify a cutoff of ks-test in the function prediction part

-----

**Script parameter list of BETA basic**

::

    -h, --help                                  show this help message and exit
    -p PEAKFILE, --peakfile PEAKFILE            The bed format of peaks binding sites. (BETA support 3
                                                or 5 columns bed format, CHROM, START, END (NAME,
                                                SCORE))
    -e EXPREFILE, --diff_expr EXPREFILE         The differential expression file get from limma for
                                                MicroArray ddata and cuffdiff for RNAseq data
    -k {LIM,CUF,BSF,O}, --kind {LIM,CUF,BSF,O}  The kind of your expression file,this is required,it
                                                can be LIM, CUF, BSF, O. LIM for LIMMA standard
                                                format. CUF for CUFDIFF standard format, BSF for BETA
                                                specific format and O for other formats, if is 'O',
                                                columns infor required via --info
    -g {hg19,mm9}, --genome {hg19,mm9}          Specify your species, hg19, mm9. For other genome
                                                assembily versions of human and mouse or other
                                                species, ignore this parameter.
    --gname2                                    If this switch is on, gene or transcript IDs in files
                                                given through -e will be considered as official gene
                                                symbols, DEFAULT=FALSE
    --info EXPREINFO                            Specify the geneID, up/down status and statistcal
                                                values column of your expression data,NOTE: use a
                                                comma as an connector. for example: 2,5,7 means geneID
                                                in the 2nd column, Tscore in 5th column and FDR in 7
                                                column DEFAULT:2,5,7 for LIMMA; 2,10,13 for Cuffdiff
                                                and 1,2,3 for BETA specific format
    -r REFERENCE, --reference REFERENCE         The refgene info file downloaded from UCSC genome
                                                browser.input this file only if your genome is neither
                                                hg19 nor mm9
    -o OUTPUT, --output OUTPUT                  The directory to store all the output files, if you
                                                don't set this, files will be output into the current
                                                directory
    --bl                                        Whether or not use CTCF boundary to filter peaks
                                                around a gene, DEFAULT=FALSE
    --bf BOUNDARYFILE                           CTCF conserved peaks bed file, use this only when you
                                                set --bl and the genome is neither hg19 nor mm9
    --pn PEAKNUMBER                             The number of peaks you want to consider,
                                                DEFAULT=10000
    --method {score,distance}                   Define the method to do the TF/CR function prediction,
                                                score for regulatory potential, distance for the
                                                distance to the proximal binding peak. DEFAULT:SCORE
    -n NAME, --name NAME                        This argument is used to name the result file.If not
                                                set, the peakfile name will be used instead
    -d DISTANCE, --distance DISTANCE            Set a number which unit is 'base'. It will get peaks
                                                within this distance from gene TSS. default:100000
                                                (100kb)
    --df DIFF_FDR                               Input a number 0~1 as a threshold to pick out the most
                                                significant differential expressed genes by FDR,
                                                DEFAULT = 1, that is select all the genes
    --da DIFF_AMOUNT                            Get the most significant differential expressed genes
                                                by the percentage(0-1) or number(larger than 1)Input a
                                                number between 0-1, the rank based on fdr for example,
                                                2000, so that the script will only consider top 2000
                                                genes as the differentially expressed genes. DEFAULT =
                                                0.5, that is select top 50 percent genes of up and
                                                down seprately. NOTE: if you want to use diff_fdr,
                                                please set this parameter to 1, otherwise it will get
                                                the intersection of these two parameters
    -c CUTOFF, --cutoff CUTOFF                  Input a number between 0~1 as a threshold to select
                                                the closer target gene list(up regulate or down
                                                regulate or both) with the p value was called by one
                                                side ks-test, DEFAULT = 0.001

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