comparison macros.xml @ 15:64ff3ef24fae draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0

14:4d8f983cd751

<macros>
    <token name="@TOOL_VERSION@">1.9.6</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@profile@">21.09</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
            <requirement type="package" version="3.0.6">loompy</requirement>

    <xml name="pl_var_names">
        <conditional name="var_names">
            <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
                <option value="all">All variables in 'adata.var_names'</option>
                <option value="custom">Subset of variables in 'adata.var_names'</option>
            </param>
            <when value="all"/>
            <when value="custom">
                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma">
                    <expand macro="sanitize_query" />
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="param_num_categories">
        <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/>

        <expand macro="pl_var_names"/>
        <expand macro="param_groupby"/>
        <expand macro="param_num_categories"/>
    </xml>
    <token name="@CMD_params_inputs@"><![CDATA[
    #if $method.var_names.type == 'all'
    var_names=adata.var_names,
    #else
    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
    var_names=$var_names,
    #end if
    #if $method.groupby
    groupby='$method.groupby',
    #end if
    num_categories=$method.num_categories,

        <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <xml name="param_n_genes">
        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
    </xml>
    <xml name="pl_dotplot">
        <param argument="color_map" type="select" optional="true" label="Color palette">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>

15:64ff3ef24fae

<macros>
    <token name="@TOOL_VERSION@">1.9.6</token>
    <token name="@VERSION_SUFFIX@">4</token>
    <token name="@profile@">21.09</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
            <requirement type="package" version="3.0.6">loompy</requirement>

    <xml name="pl_var_names">
        <conditional name="var_names">
            <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
                <option value="all">All variables in 'adata.var_names'</option>
                <option value="custom">Subset of variables in 'adata.var_names'</option>
                <option value="customfile">Subset of variables as a tabular file</option>
            </param>
            <when value="all"/>
            <when value="custom">
                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma">
                    <expand macro="sanitize_query" />
                </param>
            </when>
            <when value="customfile">
                <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
            </when>
        </conditional>
    </xml>
    <xml name="param_num_categories">
        <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/>

        <expand macro="pl_var_names"/>
        <expand macro="param_groupby"/>
        <expand macro="param_num_categories"/>
    </xml>
    <token name="@CMD_params_inputs@"><![CDATA[
    #if $method.var_names.type == 'custom'
    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
    var_names=$var_names,
    #else if $method.var_names.type == 'customfile'
    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()},
    #else
    var_names=adata.var_names,
    #end if
    #if $method.groupby
    groupby='$method.groupby',
    #end if
    num_categories=$method.num_categories,

        <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <xml name="param_n_genes">
        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
    </xml>
    <xml name="pl_dotplot">
        <param argument="color_map" type="select" optional="true" label="Color palette">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>