comparison ideas_preprocessor.xml @ 22:3651f1592f3f draft

Uploaded

21:99102499271a

    </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
mkdir $output.files_path &&
#if str($specify_chrom_windows) == "yes":
    ##############################################
    ## Using a bed file for defining chrom windows,
    ## so categorize the window positions by

    </outputs>
    <tests>
        <test>
            <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
            <param name="specify_chrom_windows" value="yes"/>
            <param name="chrom_bed_input" value="chrom_windows.bed" ftype="bed" dbkey="hg19"/>
            <output name="output" file="output.ideaspre" ftype="ideaspre" />
        </test>
    </tests>
    <help>
**What it does**

22:3651f1592f3f

    </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

    </outputs>
    <tests>
        <test>
            <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
            <param name="specify_chrom_windows" value="yes"/>
            <param name="chrom_bed_input" value="chromosomes.bed" ftype="bed" dbkey="hg19"/>
            <output name="output" file="output.html" ftype="ideaspre">
                <extra_files type="file" name="chromosomes.bed" value="chromosomes.bed"/>
                <extra_files type="file" name="chromosome_windows.txt" value="chromosome_windows.txt"/>
                <extra_files type="file" name="IDEAS_input_config.txt" value="IDEAS_input_config.txt"/>
                <extra_files type="file" name="tmp.tar" value="tmp.tar" compare="sim_size"/>
            </output>
        </test>
    </tests>
    <help>
**What it does**