comparison macros.xml @ 7:4b4dead87318 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 6da96d865a3a557cfa3ad09e1cfa830519e73748

6:db1e58e44a5c

<macros>
    <token name="@TOOL_VERSION@">0.2.4</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
        </requirements>
    </xml>

        </conditional>

    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @software{Galvis_Rodriguez_DIMet,
                    author = {Galvis Rodriguez, Johanna  and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
                    license = {MIT},
                    title = {{DIMet}},
                    url = {https://github.com/cbib/DIMet}
                    }

            </citation>
        </citations>

    </xml>
    <xml name="metadata_file_macros">

        <expand macro="isotopologue_prop_file_macros"/>
        <expand macro="metadata_file_macros"/>
    </xml>
    <xml name="input_parameters_metabologram">
        <conditional name="data_input">
            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files">
                <option value="abundance" selected="True">abundance</option>
                <option value="mean_enrichment">mean_enrichment</option>
            </param>
            <when value="abundance">
                <expand macro="abundance_file_macros"/>
                <param name="metabolites_list" type="select" optional="false" multiple="true"
                       label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
                    <validator type="length" min="1" message="Please enter at max 2 compartments"/>
                    <options from_dataset="abundance_file">
                        <column name="metabolite_or_isotopologue" index="0"/>
                        <column name="value" index="0"/>
                        <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
                        <filter type="remove_value" value="metabolite_or_isotopologue"/>
                    </options>
                    <sanitizer>
                        <valid initial="default">
                            <add preset="string.printable"/>
                            <add value="\t"/>
                            <remove value="&quot;"/>
                            <remove value="&apos;"/>
                        </valid>
                    </sanitizer>
                </param>
                <expand macro="statistical_test"/>
            </when>
            <when value="mean_enrichment">
                <expand macro="enrichment_file_macros"/>
                <param name="metabolites_list" type="select" optional="false" multiple="true"
                       label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
                    <validator type="length" min="1" message="Please enter at max 2 compartments"/>
                    <options from_dataset="me_or_frac_contrib_file">
                        <column name="metabolite_or_isotopologue" index="0"/>
                        <column name="value" index="0"/>
                        <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
                        <filter type="remove_value" value="metabolite_or_isotopologue"/>
                    </options>
                    <sanitizer>
                        <valid initial="default">
                            <add preset="string.printable"/>
                            <add value="\t"/>
                            <remove value="&quot;"/>
                            <remove value="&apos;"/>
                        </valid>
                    </sanitizer>
                </param>
                <expand macro="statistical_test"/>
            </when>
        </conditional>
        <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
        <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
        <expand macro="metadata_file_macros"/>
    </xml>
    <xml name="input_parameters_bivar_analysis">
        <conditional name="data_input">
            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
                <option value="abundance" selected="True">abundance</option>

7:4b4dead87318

<macros>
    <token name="@TOOL_VERSION@">0.2.4</token>
    <token name="@VERSION_SUFFIX@">4</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
        </requirements>
    </xml>

        </conditional>

    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btae282</citation>
            <citation type="bibtex">
                @software{Galvis_Rodriguez_DIMet,
                    author = {Galvis Rodriguez, Johanna  and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
                    license = {MIT},
                    title = {{DIMet}},
                    url = {https://github.com/cbib/DIMet}
                    }
            </citation>
        </citations>

    </xml>
    <xml name="metadata_file_macros">

        <expand macro="isotopologue_prop_file_macros"/>
        <expand macro="metadata_file_macros"/>
    </xml>
    <xml name="input_parameters_metabologram">
        <conditional name="data_input">
            <param name="data_input_selector" type="select" label="Abundance or Enrichment quantification files" help="Select between metabolite total abundances and mean enrichment files">
                <option value="abundance" selected="True">abundance</option>
                <option value="mean_enrichment">mean_enrichment</option>
            </param>
            <when value="abundance">
                <expand macro="abundance_file_macros"/>
                <expand macro="statistical_test"/>

            </when>
            <when value="mean_enrichment">
                <expand macro="enrichment_file_macros"/>
                <expand macro="statistical_test"/>
            </when>
        </conditional>
        <expand macro="metadata_file_macros"/>
        <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
        <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
    </xml>
    <xml name="input_parameters_bivar_analysis">
        <conditional name="data_input">
            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
                <option value="abundance" selected="True">abundance</option>