annotate ccqtl-permutations.xml @ 1:2df37db680ad draft default tip

planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/ccqtl commit ac8fec726c224fad58f9451042f6f62f180c8c5c

<tool id="ccqtl_permutations" name="CCQTL: Run permutations" version="@TOOL_VERSION@+@WRAPPER_VERSION@" python_template_version="3.5">
    <description>to define significance thresholds</description>
    <macros>
        <token name="@WRAPPER_VERSION@">galaxy1</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam"/>
    <expand macro="xrefs"/>
    <requirements>
        <expand macro="requirements"/>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
        @BASE_CMD@
            permutations
            --n_perm ${n_perm}
            --crossdata ${crossdata}
            --clean_pr ${clean_pr}
            --kloco ${kloco}
            --covar_modmat ${covar_modmat}
            #if $strat_covar != '':
                --strat_covar ${strat_covar}
            #end if
            ]]>
    </command>
    <inputs>
        <expand macro="crossdata"/>
        <expand macro="clean_pr"/>
        <expand macro="kloco"/>
        <param argument="--n_perm" type="integer" value="100" min="2" max="20000" label="Number of permutations (recommended minimum: 100)"/>
        <param argument="--covar_modmat" type="data" format="rds" label="covar_modmat object (rds)"/>
        <param argument="--strat_covar" type="text" value="" label="List of covariates used to stratify permutations on." help="At most three covariates, all must be categorical and previously passed as covariate at the genome_scan step. Typical stratification covariate is sex."/>
    </inputs>
    <outputs>
        <data format="rds" name="operm_lmm" from_work_dir="outfiles/Rdata/operm_lmm.rds" label="${tool.name} on ${on_string}: operm_lmm.rds"/>
        <data format="rds" name="covar_permstrata" from_work_dir="outfiles/Rdata/covar_permstrata.rds" label="${tool.name} on ${on_string}: covar_permstrata.rds"/>
        <data format="rds" name="stratcovar_modmat" from_work_dir="outfiles/Rdata/stratcovar_modmat.rds" label="${tool.name} on ${on_string}: stratcovar_modmat.rds"/>
        <data format="rds" name="nrep_rds" from_work_dir="outfiles/Rdata/nrep.rds" label="${tool.name} on ${on_string}: nrep.rds"/>
    </outputs>
    <help>
        <![CDATA[
        Compute permutations
    ]]>
    </help>
    <expand macro="citations"/>
</tool>