comparison normalize.xml @ 23:2b6498d4c8c6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy commit 732303de9670376c88e7afb2f23336ee1433e97d

22:e639abb0de92

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements">
        <requirement type="package" version="3.0.0">magic-impute</requirement>
    </expand>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@

    max_fraction=$method.exclude_highly_expressed.max_fraction,
    #end if
    #if str($method.key_added) != '':
    key_added='$method.key_added',
    #end if
    #if str($method.layer) != '':
        layer='$method.layer',
    #end if
    inplace=True)

#else if str($method.method) == 'pp.recipe_zheng17':
sc.pp.recipe_zheng17(
    adata=adata,

                    <when value="False"/>
                </conditional>
                <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored">
                    <expand macro="sanitize_query"/>
                </param>
                <param argument="layer" type="text" value="" label="Layer to normalize instead of X. If not provided, X is normalized.">
                    <expand macro="sanitize_query"/>
                </param>
            </when>
            <when value="pp.recipe_zheng17">
                <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep"/>
                <expand macro="param_log" checked="true"/>
            </when>

23:2b6498d4c8c6

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements">
        <requirement type="package" version="2.0.3">pandas</requirement>
        <requirement type="package" version="3.0.0">magic-impute</requirement>
    </expand>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@

    max_fraction=$method.exclude_highly_expressed.max_fraction,
    #end if
    #if str($method.key_added) != '':
    key_added='$method.key_added',
    #end if
    @CMD_PARAM_LAYER@
    inplace=True)

#else if str($method.method) == 'pp.recipe_zheng17':
sc.pp.recipe_zheng17(
    adata=adata,

                    <when value="False"/>
                </conditional>
                <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored">
                    <expand macro="sanitize_query"/>
                </param>
                <expand macro="param_layer" label="Layer to normalize instead of X. If not provided, X is normalized."/>
            </when>
            <when value="pp.recipe_zheng17">
                <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep"/>
                <expand macro="param_log" checked="true"/>
            </when>