comparison macs2_callpeak.xml @ 19:86e2413cf3f8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96

18:640d3af5d833

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Call peaks from alignment results</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[

            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
        </param>

        <section name="advanced_options" title="Advanced Options">
                <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
                    label="When set, scale the small sample up to the bigger sample"
                    help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
                <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming. Default: No"/>
                <param name="spmr" argument="--SPMR" type="boolean" truevalue="--SPMR" falsevalue="" checked="false"

                    <when value="broad">
                        <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
                            help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                    </when>
                    <when value="nobroad">
                        <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
                            label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
                    </when>
                </conditional>
                <expand macro="keep_duplicates" />
                <expand macro="fragment_size"/>

            <param name="qvalue" value="0.05"/>
            <param name="band_width" value="300"/>
            <param name="outputs" value="peaks_tabular,bdg,html"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <param name="lower" value="5" />
            <param name="upper" value="50" />
            <assert_command>
                <has_text text="--buffer-size"/>
                <has_text text="--d-min"/>
            </assert_command>
            <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>

            <param name="qvalue" value="0.05"/>
            <param name="band_width" value="300"/>
            <param name="outputs" value="pdf"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <param name="lower" value="5" />
            <param name="upper" value="50" />
            <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
        </test>
        <!-- Ensure BAMPE works -->
        <test expect_num_outputs="1">
            <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>

19:86e2413cf3f8

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Call peaks from alignment results</description> 
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements">
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[

            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
        </param>

        <section name="advanced_options" title="Advanced Options">
                <param argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
                    label="When set, scale the small sample up to the bigger sample"
                    help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
                <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming. Default: No"/>
                <param name="spmr" argument="--SPMR" type="boolean" truevalue="--SPMR" falsevalue="" checked="false"

                    <when value="broad">
                        <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
                            help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                    </when>
                    <when value="nobroad">
                        <param argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
                            label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
                    </when>
                </conditional>
                <expand macro="keep_duplicates" />
                <expand macro="fragment_size"/>

            <param name="qvalue" value="0.05"/>
            <param name="band_width" value="300"/>
            <param name="outputs" value="peaks_tabular,bdg,html"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <param name="mfold_lower" value="5" />
            <param name="mfold_upper" value="50" />
            <assert_command>
                <has_text text="--buffer-size"/>
                <has_text text="--d-min"/>
            </assert_command>
            <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>

            <param name="qvalue" value="0.05"/>
            <param name="band_width" value="300"/>
            <param name="outputs" value="pdf"/>
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <param name="mfold_lower" value="5" />
            <param name="mfold_upper" value="50" />
            <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/>
        </test>
        <!-- Ensure BAMPE works -->
        <test expect_num_outputs="1">
            <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>