comparison macs2_callpeak.xml @ 18:640d3af5d833 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"

17:424aefbd7777

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.6" profile="17.09">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>

            --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
        #else
            --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
        #end if


        ## With --bdg two additional output files will be generated.
        #if "bdg" in str($outputs).split(','):
            --bdg
        #end if

                        <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" />
        </section>
    </inputs>
    <outputs>
        <!--callpeaks output-->
        <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">

            <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" />
            <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
            <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
            <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
            <output name="output_extra_files">
                <assert_contents>

            <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" ftype="pdf" compare="contains" />
        </test>
        <!-- Ensure BAMPE works -->
        <test expect_num_outputs="1">
            <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>
            <param name="format" value="BAMPE" />

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>

            --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
        #else
            --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
        #end if

        --d-min $advanced_options.d_min
        --buffer-size $advanced_options.buffer_size

        ## With --bdg two additional output files will be generated.
        #if "bdg" in str($outputs).split(','):
            --bdg
        #end if

                        <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"/>
                <expand macro="buffer_size"/>
        </section>
    </inputs>
    <outputs>
        <!--callpeaks output-->
        <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">

            <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"/>
            <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
            <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
            <output name="output_extra_files">
                <assert_contents>

            <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"/>
            <param name="format" value="BAMPE" />