comparison macs2_filterdup.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_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.1">
    <description>Remove duplicate reads at the same position</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />

        #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
            --keep-dup '${ keep_dup_options.user_keepdup }'
        #else
            --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
        #end if
    ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />
        <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
        <expand macro="keep_duplicates" />

    </inputs>
    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>

18:640d3af5d833

<tool id="macs2_filterdup" name="MACS2 filterdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Remove duplicate reads at the same position</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />

        #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
            --keep-dup '${ keep_dup_options.user_keepdup }'
        #else
            --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
        #end if
        @buffer_size@
    ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />
        <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
        <expand macro="keep_duplicates" />
        <expand macro="buffer_size"/>
    </inputs>
    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>