<tool id="ideas_preprocessor" name="IDEAS preprocessor" version="1.0.0">
    <description></description>
    <requirements>
        <requirement type="package" version="2.5.4">deeptools</requirement>
        <requirement type="package" version="1.10.4">r-data.table</requirement>
        <requirement type="package" version="1.4.4">r-optparse</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
        <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set chromosome_windows = "chromosome_windows.txt"
#set ideaspre_input_config = "ideaspre_input_config.txt"
#set specify_chrom_windows = $specify_chrom_windows_cond.specify_chrom_windows
#set tmp_dir = "tmp"
mkdir $tmp_dir &&
mkdir $output.files_path &&
#if str($specify_chrom_windows) == "yes":
    ##############################################
    ## Using a bed file for defining chrom windows,
    ## so categorize the window positions by
    ## chromosome to enable the IDEAS -inv option.
    ##############################################
    cp '$gen_chromosome_windows' $chromosome_windows &&
#end if
##############################################
## Create the config file and prepare the data
##############################################
cp '$gen_ideaspre_input_config' $ideaspre_input_config &&
sort $ideaspre_input_config -o $ideaspre_input_config &&
Rscript '$__tool_directory__/ideas_preprocessor.R'
--ideaspre_input_config '$ideaspre_input_config'
#if str($specify_chrom_windows) == "yes":
    --chromosome_windows '$chromosome_windows'
    --chrom_bed_input '$specify_chrom_windows_cond.chrom_bed_input'
#else:
    --chrom_len_file '$chromInfo'
    --window_size $specify_chrom_windows_cond.window_size
    #set restrict_chromosomes = $specify_chrom_windows_cond.restrict_chromosomes_cond.restrict_chromosomes
    #if str($restrict_chromosomes) == "yes":
        #set chroms = []
        #set chrom_repeat = $specify_chrom_windows_cond.restrict_chromosomes_cond.chrom_repeat
        #for $i in $chrom_repeat.chrom
            $chroms.append($i)
        #end for
        --restrict_to_chroms ",".join(chroms)
    #end if
#end if
--reads_per_bp $reads_per_bp
#if str($exclude_input) not in ["None", ""]:
    --exclude_input '$exclude_input'
#end if
--output '$output'
--output_hid $output.hid
--output_files_path '$output.files_path'
&> ideas_preprocessor_log.txt;
if [[ $? -ne 0 ]]; then
    cp ideas_preprocessor_log.txt '$output';
   exit 1;
fi
    ]]></command>
    <configfiles>
        <configfile name="gen_ideaspre_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
    #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
    #for $i in $cell_type_epigenetic_factor_cond.input:
        #set file_name_with_ext = $i.name
        #if str($file_name_with_ext).find("http") >= 0 or str($file_name_with_ext).find("ftp") >= 0:
             #set file_name_with_ext = $file_name_with_ext.split('/')[-1]
        #end if
        #assert str($file_name_with_ext).find("-") >= 0, "The selected input '%s' is invalid because it does not include the '-' character which is required when setting cell type and epigenetic factor names by extracting them from the input file names." % $file_name_with_ext
        #set file_name = $file_name_with_ext.split(".")[0]
        #if str($input_name_positions) == "cell_first":
            #set cell_type_name = $file_name.split("-")[0]
            #set epigenetic_factor_name = $file_name.split("-")[1]
        #else:
            #set cell_type_name = $file_name.split("-")[1]
            #set epigenetic_factor_name = $file_name.split("-")[0]
        #end if
${cell_type_name} ${epigenetic_factor_name} ${i} ${file_name} ${i.ext}
    #end for
#else:
    #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
    #end for
#end if]]></configfile>
        <configfile name="gen_chromosome_windows"><![CDATA[#if str($specify_chrom_windows_cond.specify_chrom_windows) == "yes":
    #import collections
    #set window_positions_by_chroms_odict = $collections.OrderedDict()
    #for count, line in enumerate(open($specify_chrom_windows_cond.chrom_bed_input.file_name, 'r')):
        #set $line = $line.strip()
        #if not $line or $line.startswith('#'):
            #continue
        #end if
        #set items = $line.split('\t')
        #if $items[0] in $window_positions_by_chroms_odict:
            #set tup = $window_positions_by_chroms_odict[$items[0]]
            #set $tup[1] += 1
            #set $window_positions_by_chroms_odict[$items[0]] = $tup
        #else:
            #set $window_positions_by_chroms_odict[$items[0]] = [$count, $count+1]
        #end if
    #end for
    #for $chrom, $tup in $window_positions_by_chroms_odict.items():
${chrom} ${tup[0]} ${tup[1]}
    #end for
#end if]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="cell_type_epigenetic_factor_cond">
            <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
                <option value="extract" selected="true">extracting them from the selected input file names</option>
                <option value="manual">manually setting them for each selected input</option>
            </param>
            <when value="extract">
                <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig files">
                    <validator type="empty_field"/>
                    <validator type="unspecified_build"/>
                </param>
                <param name="input_name_positions" type="select" display="radio" label="Selected input file name pattern is" help="A '-' character must separate cell type and epigenetic factor names within the selected input file names">
                    <option value="cell_first" selected="true">Cell type name - Epigenetic factor name</option>
                    <option value="cell_last">Epigenetic factor name - Cell type name</option>
                </param>
            </when>
            <when value="manual">
                <repeat name="input_repeat" title="Cell type, Epigenetic factor and Input" min="1">
                    <param name="cell_type_name" type="text" value="" label="Cell type name">
                        <validator type="empty_field"/>
                    </param>
                    <param name="epigenetic_factor_name" type="text" value="" label="Epigenetic factor name">
                        <validator type="empty_field"/>
                    </param>
                    <param name="input" type="data" format="bigwig,bam" label="BAM or BigWig file">
                        <validator type="empty_field"/>
                        <validator type="unspecified_build"/>
                    </param>
                </repeat>
            </when>
        </conditional>
        <conditional name="specify_chrom_windows_cond">
            <param name="specify_chrom_windows" type="select" label="Define chromosome window positions from a bed file?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
                <param name="window_size" type="integer" value="200" label="Window size in base pairs"/>
                <conditional name="restrict_chromosomes_cond">
                    <param name="restrict_chromosomes" type="select" label="Restrict processing to specified chromosomes">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no"/>
                    <when value="yes">
                        <repeat name="chrom_repeat" title="Chromosomes" min="1">
                            <param name="chrom" type="text" value="" label="Chromosome" help="One chromosome (e.g., chr1, chr2, chrX) per text field"/>
                        </repeat>
                    </when>
                </conditional>
            </when>
            <when value="yes">
                <param name="chrom_bed_input" type="data" format="bed" label="Bed file for defining the chromosome window positions">
                    <validator type="empty_dataset"/>
                </param>
            </when>
        </conditional>
        <param name="bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
        <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each window using">
            <option value="6" selected="true">mean</option>
            <option value="8">max</option>
        </param>
        <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
        <param name="standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
    </inputs>
    <outputs>
        <data name="output" format="ideaspre"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

-----

**Required options**

    </help>
    <citations>
        <citation type="doi">10.1093/nar/gkw278</citation>
    </citations>
</tool>