Mercurial > repos > rplanel > ccqtl_permutations

<macros>
    <token name="@TOOL_VERSION@">0.0.1_beta.2</token>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">ccqtl</xref>
        </xrefs>
    </xml>
    <xml name="edam">
        <edam_topics>
            <edam_topic>topic_0625</edam_topic>
            <edam_topic>topic_0160</edam_topic>
            <edam_topic>topic_3338</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_3232</edam_operation>
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirement type="package" version="@TOOL_VERSION@">r-ccqtl</requirement>
        <yield/>
    </xml>
    <token name="@BASE_CMD@">
        ccqtl --cores \${GALAXY_SLOTS:-1}
    </token>
    <xml name="indiv_marker">
        <param name="indiv_marker" argument="--indiv_geno" type="select" label="Select individual genotypes of each CC mouse at each marker" help="Directory that contains the individual genotypes of each CC mouse at each marker and the funnel codes if applicable.">
            <options from_data_table="ccqtl">
                <filter type="static_value" column="1" value="indiv_marker"/>
                <validator type="no_options" message="No dataset available for the selected input dataset"/>
            </options>
        </param>
    </xml>
    <xml name="marker_set">
        <param argument="--marker_set" type="select" label="Select the genetic and physical maps as well as the founder genotypes information" help="Directory that contains the genetic and physical maps as well as the founder genotypes information, for the different combinations of marker set and genome build.">
            <options from_data_table="ccqtl">
                <filter type="static_value" column="1" value="marker_set"/>
                <validator type="no_options" message="No dataset available for the selected input dataset"/>
            </options>
        </param>
    </xml>
    <xml name="crossdata">
        <param argument="--crossdata" type="data" format="rds" label="crossdata rds file" help="The cross rds file output from make_inputs"/>
    </xml>
    <xml name="kloco">
        <param argument="--kloco" type="data" format="rds" label="kloco rds file" help="the LOCO kinship rds file output from make_inputs"/>
    </xml>
    <xml name="clean_pr">
        <param argument="--clean_pr" type="data" format="rds" label="clean_pr ds file" help="The cleaned genotype probabilities rds file output from make_inputs"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{githubseqtk,
                author = {Victoire Baillet, Rémi Planel, Vincent Guillemot, Pascal Campagne},
                year = {2023},
                title = {ccqtl},
                publisher = {Gitlab},
                journal = {Gitlab repository},
                url = {https://gitlab.pasteur.fr/cc-qtl/ccqtl},
                }</citation>
        </citations>
    </xml>
</macros>
author	rplanel
date	Fri, 29 Sep 2023 14:58:06 +0000
parents	6b6c9ab21674
children