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<tool id="beta_plus" name="BETA-plus: Binding and Expression Target prediction and motif analysis" version="0.1.0">
  <description>Predict the factors (TFs or CRs) direct target genes by combining the binding and expression data, then do motif analysis on target regions</description>
  <macros>
    <import>beta_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
  BETA plus 
  #include source=$common_opts#
  #include source=$genome_opts#
  #include source=$ref_genome_seq_opts#
  #include source=$extended_opts#
  --mn $motifs
  &amp;> $log &amp;&amp;
  mkdir -p $motifresult.extra_files_path  &amp;&amp;
  cp BETA_OUTPUT/motifresult/betamotif.html $motifresult  &amp;&amp;
  cp BETA_OUTPUT/motifresult/*.js $motifresult.extra_files_path &amp;&amp;
  cp BETA_OUTPUT/motifresult/*.css $motifresult.extra_files_path &amp;&amp;
  cp -r BETA_OUTPUT/motifresult/img $motifresult.extra_files_path

  </command>
  <inputs>
    <expand macro="common_params" />
    <expand macro="genome_params" />
    <expand macro="refGenomeSourceConditional" />
    <expand macro="extended_params" />
    <param name="motifs" type="float" value="10" optional="true" label="Motifs to retrieve" 
           help="a number between 0 and 1 as the p-value cutoff or an integer larger than 1 as the number of motifs">
        <validator type="in_range" max="20000" min="0" message="A float between 0 and 1 or an integer greater than 1" />
    </param>
  </inputs>
  <expand macro="stdio" />
  <outputs>
    <data format="txt" name="log" label="Log of BETA plus"/>
    <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"/>
    <data format="txt" name="upmotifs" label="BETA Motifs in up-target regions" from_work_dir="BETA_OUTPUT/motifresult/UP_MOTIFS.txt" />
    <data format="txt" name="up_non_motifs" label="BETA Motifs in up-target regions versus non-target regions" from_work_dir="BETA_OUTPUT/motifresult/UP_NON_MOTIFS.txt" />
    <data format="txt" name="downmotifs" label="BETA Motifs in down-target regions" from_work_dir="BETA_OUTPUT/motifresult/DOWN_MOTIFS.txt" />
    <data format="txt" name="down_non_motifs" label="BETA Motifs in down-target regions versus non-target regions" from_work_dir="BETA_OUTPUT/motifresult/DOWN_NON_MOTIFS.txt" />
    <data format="txt" name="differentialmotifs" label="BETA Motifs up-target regions versus down-target regions" from_work_dir="BETA_OUTPUT/motifresult/DIFFERENTIAL_MOTIF_UP_DOWN.txt" />
    <data format="html" name="motifresult" label="BETA Motif analysis on target regions"/>
  </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" type="text" 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="NM_001002231" />
        </assert_contents>
      </output>
      <output name="downtargetsoutput">
        <assert_contents>
            <has_text_matching expression="NM_001280" />
        </assert_contents>
      </output>
      <output name="differentialmotifs">
        <assert_contents>
            <has_text_matching expression="CDX1\tHomeodomain Family" />
        </assert_contents>
      </output>
    </test>
  </tests>
 <help>
** BETA plus **

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

This tool annotates the given intervals and scores with genome
features such as gene body. 
Predicts Direct targets of TF and the active/repressive function
prediction.  Does motif analysis at targets region as well. 
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.
- **genomereference** Genome reference data with fasta format
- **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 plus**

::

  -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
  --gs GENOMEREFERNCE	GenomeReference file with fasta format
  --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>
</tool>