comparison macs2_callpeak.xml @ 3:6d4babad010f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316

2:bfe57d6e0c4c

    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
        <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>

            ##--shiftsize '$nomodel_type.shiftsize'
            --extsize '${ nomodel_type.extsize }'
        #end if

        2> $temp_stderr)
        #if 'peaks_bed' in str($outputs).split(','):
            &&
            awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3  > "${ output_bed }"
        #end if

        ## run R to create pdf from model script
        #if $nomodel_type.nomodel_type_selector == 'create_model' and 'pdf' in str($outputs).split(','):
            &&

                    help="MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of legacy shiftsize. In previous language, each read is moved 3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 3' into a d size fragment. DEFAULT: 200 (--extsize)"/>
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
            <option value="peaks_bed" selected="True">Peaks as BED file</option>
            <!--<option value="narrow">narrow Peaks</option>-->
            <option value="summits" selected="true">summits</option>
            <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF</option>

            <when value="off" />
        </conditional>
    </inputs>
    <outputs>
        <!--callpeaks output-->
        <data name="output_bed" format="bed" label="${tool.name} on ${on_string} (Peaks in BED format)">
            <filter>'peaks_bed' in outputs</filter>
        </data>
        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
            <filter>
            ((
              advanced_options['advanced_options_selector'] == "on" and
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
            <filter>
            ((
              advanced_options['advanced_options_selector'] == "on" and
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
            <filter>
            (
              advanced_options['advanced_options_selector'] == "off" or
            (
              advanced_options['advanced_options_selector'] == "on" and

            <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
            <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
            <param name="cutoff_options_selector" value="qvalue"/>
            <param name="qvalue" value="0.05"/>
            <param name="band_width" value="300"/>
            <param name="outputs" value="peaks_bed,bdg"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg"/>
            <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg"/>
            <output name="output_bed" compare="contains" file="callpeak_part.bed"/>
            <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/>
        </test>
        <test>
            <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
            <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>

3:6d4babad010f

    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>

            ##--shiftsize '$nomodel_type.shiftsize'
            --extsize '${ nomodel_type.extsize }'
        #end if

        2> $temp_stderr)
        #if 'peaks_tabular' in str($outputs).split(','):
            &&
            cp MACS2_peaks.xls "${ output_tabular }"
        #end if

        ## run R to create pdf from model script
        #if $nomodel_type.nomodel_type_selector == 'create_model' and 'pdf' in str($outputs).split(','):
            &&

                    help="MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of legacy shiftsize. In previous language, each read is moved 3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 3' into a d size fragment. DEFAULT: 200 (--extsize)"/>
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs" help="PDF only created when model is build">
            <option value="peaks_tabular" selected="True">Peaks as tabular file</option>
            <!--<option value="narrow">narrow Peaks</option>-->
            <option value="summits" selected="true">summits</option>
            <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option>
            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF</option>

            <when value="off" />
        </conditional>
    </inputs>
    <outputs>
        <!--callpeaks output-->
        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)">
            <filter>'peaks_tabular' in outputs</filter>
        </data>
        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
            <filter>
            ((
              advanced_options['advanced_options_selector'] == "on" and
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
            <filter>
            ((
              advanced_options['advanced_options_selector'] == "on" and
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
            <filter>
            (
              advanced_options['advanced_options_selector'] == "off" or
            (
              advanced_options['advanced_options_selector'] == "on" and

            <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
            <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
            <param name="cutoff_options_selector" value="qvalue"/>
            <param name="qvalue" value="0.05"/>
            <param name="band_width" value="300"/>
            <param name="outputs" value="peaks_tabular,bdg"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg"/>
            <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg"/>
            <output name="output_tabular" compare="contains" file="callpeak_part.tabular"/>
            <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/>
        </test>
        <test>
            <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
            <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>