comparison macros.xml @ 47:1cd9574ee4f8 draft default tip

planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d

46:67f0ef6236f1

    </token>

    <xml name="input_file_load">
        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
                    <option value="no" >no need</option>
                    <option value="yes" >yes</option>
                </param>
                <when value="no">
                </when>
                <when value="yes">
                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

    <xml name="test_file_load_single">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <!-- peaklist export option management -->

            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
            <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
                <option value="into" selected="true">into</option>
                <option value="maxo" >maxo</option>
                <option value="intb">intb</option>
            </param>
        </section>
    </xml>

            <param name="ppm" value="5"/>
            <param name="mzabs" value="0.015"/>
            <param name="max_peaks" value="100"/>
        </section>
        <section name="diffreport">
        <conditional name="options">
            <param name="option" value="show"/>
            <param name="eicmax" value="200"/>
            <param name="eicwidth" value="200"/>
            <param name="value" value="into"/>
            <param name="h" value="480"/>
            <param name="w" value="640"/>
            <param name="mzdec" value="2"/>
            <param name="sortpval" value="False"/>
            <param name="tabular2" value="zip"/>
            <param name="png2" value="zip"/>
        </conditional>
        </section>
        <expand macro="test_peaklist"/>
    </xml>

    <xml name="test_annotate_quick_false">

---------------------------------------------------

    </token>

    <token name="@HELP_CAMERA_NEWVERSION_1480@">
**Version 2.2.6+camera1.48.0 - 11/06/2021**

- UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
    </token>

        <citations>
            <citation type="doi">10.1021/ac202450g</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>
</macros>

47:1cd9574ee4f8

    </token>

    <xml name="input_file_load">
        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server.">
                    <option value="no">no need</option>
                    <option value="yes">yes</option>
                </param>
                <when value="no">
                </when>
                <when value="yes">
                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

    <xml name="test_file_load_single">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <xml name="test_file_load_faahKO_15">
        <section name="file_load_section">
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes" />
                <param name="input" value="wt15.CDF,ko15.CDF" ftype="netcdf" />
            </conditional>
        </section>
    </xml>

    <!-- peaklist export option management -->

            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
            <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
                <option value="into" selected="true">into</option>
                <option value="maxo">maxo</option>
                <option value="intb">intb</option>
            </param>
        </section>
    </xml>

            <param name="ppm" value="5"/>
            <param name="mzabs" value="0.015"/>
            <param name="max_peaks" value="100"/>
        </section>
        <section name="diffreport">
            <conditional name="options">
                <param name="option" value="show"/>
                <param name="eicmax" value="200"/>
                <param name="eicwidth" value="200"/>
                <param name="value" value="into"/>
                <param name="h" value="480"/>
                <param name="w" value="640"/>
                <param name="mzdec" value="2"/>
                <param name="sortpval" value="False"/>
                <param name="tabular2" value="zip"/>
                <param name="png2" value="zip"/>
            </conditional>
        </section>
        <expand macro="test_peaklist"/>
    </xml>

    <xml name="test_annotate_quick_false">

---------------------------------------------------

    </token>

    <token name="@HELP_CAMERA_SUITE@">
**Version 0.1.0+camera1.48.0 - 06/11/2024**

- Initial release with core functionalities for peak annotation, grouping, and visualization using CAMERA (see CAMERA News_).
    </token>

    <token name="@HELP_CAMERA_NEWVERSION_1480@">
**Version 2.2.6+camera1.48.0 - 11/06/2021**

- UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
    </token>

        <citations>
            <citation type="doi">10.1021/ac202450g</citation>
            <citation type="doi">10.1093/bioinformatics/btu813</citation>
        </citations>
    </xml>

    <xml name="creator">
        <creator>
            <organization name="MELISA" url="https://www.laberca.org/plateforme-melisa/presentation"></organization>
            <organization name="Workflow4metabolomics" url="https://workflow4metabolomics.org/"></organization>

            <person givenName="Yann" familyName="Guitton" url="https://github.com/yguitton"></person>
            <person givenName="Damien" familyName="Rat" url="https://github.com/DamienCode404"></person>
            <person givenName="Julien" familyName="Saint-Vanne" url="https://github.com/jsaintvanne"></person>
        </creator>
    </xml>
</macros>