comparison macros.xml @ 11:73ab2ac53d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d

10:bf2017df9837

<macros>
    <token name="@version@">1.7.1</token>
    <token name="@profile@">19.01</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@version@">scanpy</requirement>
            <requirement type="package" version="2.0.17">loompy</requirement>
            <requirement type="package" version="0.8.3">leidenalg</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">scanpy</xref>
        </xrefs>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s13059-017-1382-0</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>

    </xml>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read('anndata.h5ad')
]]>
    </token>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Options" expanded="false">
            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
        </section>
    </xml>
    <xml name="anndata_outputs">
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
        <data name="hidden_output" format="txt" label="Log file" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
adata.write('anndata.h5ad')
with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
    print(adata, file=ainfo)
]]>
    </token>
    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'

            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_color_map">
        <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
            <option value="None">Default</option>
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_frameon">
        <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>

    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    @CMD_param_legend_fontsize@
    legend_fontweight='$method.plot.legend_fontweight',
    @CMD_param_size@
    #if str($method.plot.color_map) != 'None'
    color_map='$method.plot.color_map',
    #end if
    #if str($method.plot.palette) != ''
    palette='$method.plot.palette',
    #end if

11:73ab2ac53d06

<macros>
    <token name="@version@">1.9.6</token>
    <token name="@profile@">22.05</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@version@">scanpy</requirement>
            <requirement type="package" version="3.0.6">loompy</requirement>
            <requirement type="package" version="0.10.1">leidenalg</requirement>
            <requirement type="package" version="0.8.1">louvain</requirement>
            <requirement type="package" version="1.5.3">pandas</requirement>
            <requirement type="package" version="3.7">matplotlib</requirement>
            <requirement type="package" version="0.12.2">seaborn</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">scanpy</xref>
        </xrefs>
    </xml>
    <xml name="creators">
        <creator>
            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
        </creator>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s13059-017-1382-0</citation>
            <citation type="doi">10.1093/gigascience/giaa102</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>

    </xml>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read_h5ad('anndata.h5ad')
]]>
    </token>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Options" expanded="false">
            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
        </section>
    </xml>
    <xml name="anndata_outputs">
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
            <data name="hidden_output" format="txt" label="Log file" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
adata.write_h5ad('anndata.h5ad')
with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
    print(adata, file=ainfo)
]]>
    </token>
    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'

            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_color_map">
        <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
            <option value="" >Default</option>
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_frameon">
        <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>

    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    @CMD_param_legend_fontsize@
    legend_fontweight='$method.plot.legend_fontweight',
    @CMD_param_size@
    #if str($method.plot.color_map) != ''
    color_map='$method.plot.color_map',
    #end if
    #if str($method.plot.palette) != ''
    palette='$method.plot.palette',
    #end if