comparison ideas_preprocessor.xml @ 4:f577a83e86c4 draft

Uploaded

3:e97851e8951b

        <requirement type="package" version="1.6">samtools</requirement>
        <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set tmp_dir = "tmp"
#set prep_input_config = "prep_input_config.txt"
#set prep_output_config = "prep_output_config.txt"
#set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
mkdir $tmp_dir &&
mkdir $output.files_path &&
#if str($specify_genomic_window) == "yes":
    ##############################################
    ## Using a genomic window bed file, so categorize
    ## the window positions by chromosome to enable
    ## the IDEAS -inv option.
    ##############################################
    #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
    cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config &&
#end if
##############################################
## Create the config file and prepare the data
##############################################
cp '$gen_prep_input_config' $prep_input_config &&
sort $prep_input_config -o $prep_input_config &&
Rscript '$__tool_directory__/ideas_preprocessor.R'
--prep_input_config '$prep_input_config'
#if str($specify_genomic_window) == "yes":
    --prep_output_config '$prep_output_config'
    --windows_positions_by_chroms_config '$windows_positions_by_chroms_config'
#end if
#if str($specify_genomic_window) == "yes":
    --bed_input '$specify_genomic_window_cond.bed_input'
#else:
    --chrom_len_file '$chromInfo'
    --window_size $specify_genomic_window_cond.window_size
    #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
    #if str($restrict_chromosomes) == "yes":
        #set chroms = []
        #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
        #for $i in $chrom_repeat.chrom
            $chroms.append($i)
        #end for
        --restrict_to_chroms ",".join(chroms)
    #end if

--reads_per_bp $reads_per_bp
#if str($exclude_input) not in ["None", ""]:
    --exclude_input '$exclude_input'
#end if
--output '$output'
--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_prep_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]

#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} ${input_items.input.ext}
    #end for
#end if]]></configfile>
        <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":
    #import collections
    #set window_positions_by_chroms_odict = $collections.OrderedDict()
    #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
        #set $line = $line.strip()
        #if not $line or $line.startswith('#'):
            #continue
        #end if
        #set items = $line.split('\t')

                        <validator type="unspecified_build"/>
                    </param>
                </repeat>
            </when>
        </conditional>
        <conditional name="specify_genomic_window_cond">
            <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
                <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"/>

                        </repeat>
                    </when>
                </conditional>
            </when>
            <when value="yes">
                <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/>
            </when>
        </conditional>
        <param argument="--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 genomic window using">
            <option value="6" selected="true">mean</option>

        </param>
        <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
        <param argument="--standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
    </inputs>
    <outputs>
        <data name="output" format="html"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>

4:f577a83e86c4

        <requirement type="package" version="1.6">samtools</requirement>
        <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set tmp_dir = "tmp"
#set ideaspre_input_config = "ideaspre_input_config.txt"
#set ideas_input_config = "IDEAS_input_config.txt"
#set specify_chrom_window = $specify_chrom_window_cond.specify_chrom_window
mkdir $tmp_dir &&
mkdir $output.files_path &&
#if str($specify_chrom_window) == "yes":
    ##############################################
    ## Using a genomic window bed file, so categorize
    ## the window positions by chromosome to enable
    ## the IDEAS -inv option.
    ##############################################
    #set chromosome_windows = "chromosome_windows.txt"
    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_window) == "yes":
    --ideas_input_config '$ideas_input_config'
    --chromosome_windows '$chromosome_windows'
#end if
#if str($specify_chrom_window) == "yes":
    --chrom_bed_input '$specify_chrom_window_cond.chrom_bed_input'
#else:
    --chrom_len_file '$chromInfo'
    --window_size $specify_chrom_window_cond.window_size
    #set restrict_chromosomes = $specify_chrom_window_cond.restrict_chromosomes_cond.restrict_chromosomes
    #if str($restrict_chromosomes) == "yes":
        #set chroms = []
        #set chrom_repeat = $specify_chrom_window_cond.restrict_chromosomes_cond.chrom_repeat
        #for $i in $chrom_repeat.chrom
            $chroms.append($i)
        #end for
        --restrict_to_chroms ",".join(chroms)
    #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]

#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_window_cond.specify_chrom_window) == "yes":
    #import collections
    #set window_positions_by_chroms_odict = $collections.OrderedDict()
    #for count, line in enumerate(open($specify_chrom_window_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')

                        <validator type="unspecified_build"/>
                    </param>
                </repeat>
            </when>
        </conditional>
        <conditional name="specify_chrom_window_cond">
            <param name="specify_chrom_window" type="select" label="Specify window positions using 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"/>

                        </repeat>
                    </when>
                </conditional>
            </when>
            <when value="yes">
                <param name="chrom_bed_input" type="data" format="bed" label="Bed file specifying the window positions"/>
            </when>
        </conditional>
        <param argument="--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 genomic window using">
            <option value="6" selected="true">mean</option>

        </param>
        <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
        <param argument="--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>