view beta_minus.xml @ 5:c119110a5b47 draft default tip

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

<tool id="beta_minus" name="BETA-minus: Targets prediction with binding only" version="@VERSION@.0">
    <description>Predict the factors (TFs or CRs) direct target genes by only binding data</description>
    <macros>
        <import>beta_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
        BETA minus 
        #include source=$common_opts#
        #include source=$genome_opts#
        #include source=$write_log#
    ]]></command>
    <inputs>
        <expand macro="common_params" />
        <expand macro="genome_params" />
    </inputs>
    <outputs>
        <data format="txt" name="log" label="Log of BETA minus"/>
        <data format="tabular" name="targetsoutput" label="BETA predicted Targets" from_work_dir="BETA_OUTPUT/NA_targets.txt"/>
        <data format="tabular" name="targetpeaks" label="BETA Target gene's associated peaks" from_work_dir="BETA_OUTPUT/NA_targets_associated_peaks.txt"/>
    </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"/>
            <output name="log">
                <assert_contents>
                        <has_text_matching expression="Finished" />
                </assert_contents>
            </output>
            <output name="targetsoutput">
                <assert_contents>
                        <has_text_matching expression="chr19\t4675243\t4723855\tNM_139159\t1.1.*\t-\tDPP" />
                </assert_contents>
            </output>
            <output name="targetpeaks">
                <assert_contents>
                        <has_text_matching expression="chr19\t4723422\t4724314\tregion_9\tNM_139159\tDPP9\t13\t0.6.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
 <help><![CDATA[
** BETA minus **

@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.
- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter.
- **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
- **NAME** specify the name of the output files.
- **DISTANCE** specify the distance wich peaks within it will be considered.


-----

**script parameter list of BETA minus**

::

    -h, --help                        show this help message and exit
    -p PEAKFILE, --peakfile PEAKFILE
                                                The bed format of peaks binding sites. 
                                                BETA supports 3 or 5 columns bed format: CHROM, START, END [NAME, SCORE]
    -g {hg19,mm9}, --genome {hg19,mm9}
                                                Specify your species, {hg19, mm9}
    -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
    --pn PEAKNUMBER             the number of peaks you want to consider, DEFAULT=10000
    -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)

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