<tool id="span" name="SPAN" version="0.7.1.4272">
    <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
    <requirements>
        <requirement type="package" version="0.7.1.4272">package_span_jar</requirement>
    </requirements>
    <stdio>
        <!-- Wrapper ensures anything other than zero is an error -->
        <exit_code range="1:"/>
        <exit_code range=":-1"/>
    </stdio>
    <command interpreter="python">
#import re
#set treatment_identifier = re.sub('[^\w\-\.]', '_', str($treatment_file.element_identifier))
#set genome_identifier = re.sub('[^\w\-\.]', '_', str($genome_file.element_identifier))

#if $control.control_selector
    #set control_identifier = re.sub('[^\w\-\.]', '_', str($control.control_file.element_identifier))
#end if

#if str($action.action_selector) == "model"
    #if $control.control_selector
        span_wrapper.py model with_control
            "${genome_identifier}" "${genome_file}"
            "${treatment_identifier}" "${treatment_file}"
            "${bin}" "${action.model_file}"
            "${control_identifier}" "${control.control_file}"
    #else
        span_wrapper.py model without_control
            "${genome_identifier}" "${genome_file}"
            "${treatment_identifier}" "${treatment_file}"
            "${bin}" "${action.model_file}"
    #end if
#else
    #if $control.control_selector
        span_wrapper.py peaks with_control
            "${genome_identifier}" "${genome_file}"
            "${treatment_identifier}" "${treatment_file}"
            "${bin}" "${action.model_file}"
            "${control_identifier}" "${control.control_file}"
            "${action.fdr}" "${action.gap}" "${action.peaks_file}"
    #else
        span_wrapper.py peaks without_control
            "${genome_identifier}" "${genome_file}"
            "${treatment_identifier}" "${treatment_file}"
            "${bin}" "${action.model_file}"
            "${action.fdr}" "${action.gap}" "${action.peaks_file}"
    #end if
#end if
     </command>
    <inputs>
        <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
               description="Treatment BAM reads to process" argument="--treatment"
               help="Treatment BAM reads to process"/>
        <param name="genome_file" type="data" format="chrom.sizes" label="Genome chrom.sizes"
               description="Genome build chrom.sizes file" argument="--chrom.sizes"
               help="Genome build chrom.sizes file"/>

        <conditional name="control">
            <param name="control_selector" type="boolean" label="Control available" value="false"/>
            <when value="true">
                <param name="control_file" type="data" format="bam" label="Control BAM"
                       description="Control BAM reads to process" argument="--control"
                       help="Control BAM reads to process"/>
            </when>
        </conditional>

        <conditional name="action">
            <param name="action_selector" type="select" label="Action">
                <option value="model">Compute SPAN model</option>
                <option value="peaks">Compute SPAN model and produce peaks file</option>
            </param>
            <when value="model">
                <param name="model_file" type="text" value="model.span" label="Model name"
                       help="Trained model file in binary format, which can be visualized directly in JBR Genome Browser
                       and used in integrated peak calling pipeline"/>
            </when>
            <when value="peaks">
                <param name="model_file" type="text" value="model.span" label="Model file name"
                       help="Trained model file in binary format, which can be visualized directly in JBR Genome Browser
                       and used in integrated peak calling pipeline"/>
                <param name="fdr" size="5" type="float" value="0.0001" label="FDR" argument="--fdr"
                       help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
                       SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
                       Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
                       Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
                       q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
                <param name="gap" size="5" type="integer" value="5" label="GAP" argument="--gap"
                       help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
                       Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
                <param name="peaks_file" type="text" value="result.peak" label="Peaks file name" argument="--peaks"/>
            </when>
        </conditional>

        <param name="bin" size="5" type="integer" value="200" label="Bin size" argument="--bin"
               help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
               Default value is 200bp, approximately the length of one nucleosome."/>
    </inputs>
    <outputs>
        <data name="SPAN model file" format="span" from_work_dir="*.span" label="SPAN model file ${action.model_file} on ${on_string}"/>
        <data name="SPAN peaks file" format="bed" from_work_dir="*.peak" label="SPAN peaks file ${action.peaks_file} on ${on_string}">
            <filter>action['action_selector'] == "peaks"</filter>
        </data>
        <data name="SPAN log file" format="txt" from_work_dir="*.log" label="SPAN log file on ${on_string}"/>
    </outputs>
    <help><![CDATA[
.. class:: infomark

**What it does**

SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.

-----

**Inputs**

*-t, --treatment <Path>*        **Required.** ChIP-seq treatment file. bam, bed or .bed.gz file; If multiple files are given, treated as replicates.

*--chrom.sizes, --cs <Path>*    **Required.** Chromosome sizes path, can be downloaded at http://hgdownload.cse.ucsc.edu/goldenPath/<build>/bigZips/<build>.chrom.sizes

*-c, --control <Path>*          Control file. bam, bed or bed.gz file; Single control file or separate file per each treatment file required.

*--fragment <Integer>*          Fragment size, read length if not given

*-b, --bin <Integer>*           Bin size

*-f, --fdr <Double>*            Fdr value

*-g, --gap <Integer>*           Gap size to merge peaks

*-p, --peaks <Path>*            Path to result peaks file in ENCODE broadPeak (BED 6+3) format


-----

**Outputs**

This tool produces a SPAN binary model file and/or peaks in ENCODE broadPeak (BED 6+3) format.

Peak file columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak
* **3rd**: end position of peak
* **4th**: name of peak
* **5th**: integer score for display in genome browser (e.g. UCSC)
* **6th**: strand, either "." (=no strand) or "+" or "-"
* **7th**: fold-change
* **8th**: -log10pvalue
* **9th**: -log10qvalue

-----

**SPAN workflow**

* Convert raw reads to tags using *FRAGMENT* parameter.
* Compute coverage for all genome tiled into bins of *BIN* base pairs.
* Fit 3-state hidden Markov model that classifies bins as ZERO states with no coverage, LOW states of non-specific binding, and HIGH states of the specific binding.
* Compute posterior HIGH state probability of each bin.
* Trained model is saved into *.span* binary format.
* Peaks are computed using trained model and *FDR* and *GAP* parameters.

------

**Citation**

If you use this tool in Galaxy, please cite XXX, et al. *In preparation.*

-----

**More Information**

* Project home page: https://research.jetbrains.org/groups/biolabs/tools/span-peak-analyzer
* Study cases: https://artyomovlab.wustl.edu/aging

]]></help>
</tool>