comparison macros.xml @ 18:38db3fef7aad draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634

17:178242b82297

            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
            <requirement type="package" version="0.10.3">anndata</requirement>
            <requirement type="package" version="1.26.4">numpy</requirement>
            <requirement type="package" version="2.2.2">pandas</requirement>
            <requirement type="package" version="1.14.1">scipy</requirement>
            <requirement type="package" version="0.14.2">statsmodels</requirement>           
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>

        <citations>
            <citation type="doi">10.1186/s13059-017-1382-0</citation>
            <citation type="doi">10.1093/gigascience/giaa102</citation>
        </citations>
    </xml>
    
    
    <!-- param macros -->
    <xml name="sanitize_query" token_validinitial="string.printable">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <remove value="&apos;"/>

        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <add value=","/>
            </valid>
        </sanitizer>
    </xml>      
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Options" expanded="false">

            <yield />
        </data>
        <data name="hidden_output" format="txt" label="Log file" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>    
    <xml name="param_use_rep">
        <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
                <expand macro="sanitize_query"/>
        </param>
    </xml>

        <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
    </xml>
    <!-- param macros -->


    
    <!-- command macros -->
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>
    <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[

    size=$method.violin_plot.stripplot.jitter.size,
    #end if
#end if
    ]]>
    </token>
    
    <xml name="params_seaborn_violinplot">
        <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
            <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth">
                <option value="scott" selected="true">scott</option>
                <option value="silverman">silverman</option>

    #if $method.seaborn_violinplot.color:
    color='$method.seaborn_violinplot.color',
    #end if
    saturation=$method.seaborn_violinplot.saturation,
    ]]></token>
   
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query"/>
        </param>
    </xml>

    #end for
    components=$components,
#end if
    ]]>
    </token>
    
    <xml name="param_legend_fontsize">
        <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/>
    </xml>
    <token name="@CMD_PARAM_LEGEND_FONTSIZE@"><![CDATA[
    #if str($method.plot.legend_fontsize) != '':

18:38db3fef7aad

            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
            <requirement type="package" version="0.10.3">anndata</requirement>
            <requirement type="package" version="1.26.4">numpy</requirement>
            <requirement type="package" version="2.2.2">pandas</requirement>
            <requirement type="package" version="1.14.1">scipy</requirement>
            <requirement type="package" version="0.14.2">statsmodels</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>

        <citations>
            <citation type="doi">10.1186/s13059-017-1382-0</citation>
            <citation type="doi">10.1093/gigascience/giaa102</citation>
        </citations>
    </xml>


    <!-- param macros -->
    <xml name="sanitize_query" token_validinitial="string.printable">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <remove value="&apos;"/>

        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <add value=","/>
            </valid>
        </sanitizer>
    </xml>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Options" expanded="false">

            <yield />
        </data>
        <data name="hidden_output" format="txt" label="Log file" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>
    <xml name="param_use_rep">
        <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
                <expand macro="sanitize_query"/>
        </param>
    </xml>

        <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
    </xml>
    <!-- param macros -->



    <!-- command macros -->
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>
    <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[

    size=$method.violin_plot.stripplot.jitter.size,
    #end if
#end if
    ]]>
    </token>

    <xml name="params_seaborn_violinplot">
        <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
            <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth">
                <option value="scott" selected="true">scott</option>
                <option value="silverman">silverman</option>

    #if $method.seaborn_violinplot.color:
    color='$method.seaborn_violinplot.color',
    #end if
    saturation=$method.seaborn_violinplot.saturation,
    ]]></token>

    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query"/>
        </param>
    </xml>

    #end for
    components=$components,
#end if
    ]]>
    </token>

    <xml name="param_legend_fontsize">
        <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/>
    </xml>
    <token name="@CMD_PARAM_LEGEND_FONTSIZE@"><![CDATA[
    #if str($method.plot.legend_fontsize) != '':