comparison macros.xml @ 4:050cfef6ba65 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed

3:2ec9253a647e

<macros>
    <token name="@TOOL_VERSION@">1.2.4</token>

    <xml name="creator">
        <creator>
            <person
                givenName="Helge"

            <person
                givenName="Martin"
                familyName="Čech"
                url="https://github.com/martenson"
                identifier="0000-0002-9318-1781" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI"/>
        </creator>

        <section name="ms_csv" title="Input MS Data as CSV" expanded="true">
            <param label="Input CSV" name="ms" type="data" format="csv"
                   help="Features as columns, rows as samples. Column header in format mz_rt."/>
            <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true"
                   help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/>
        </section>
    </xml>

    <xml name="parameters_xcms">
        <section name="xcms" title="Input MS Data as XCMS" expanded="true">
            <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks"
                   help="Grouped feature data for clustering." />
            <param label="Preserve phenotype" name="usePheno" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
                   help="Transfer phenotype data from XCMS object to Spec abundance file."/>
        </section>
    </xml>

    <xml name="parameters_required">
        <param label="Sigma r" name="sr" type="float" value="0.5" help="Correlational similarity between features."/>
        <param label="Correlation method" name="cor_method" type="select" display="radio"
               help="Choose correlational method to be used - see [1] for details.">
            <option value="pearson" selected="true">pearson</option>
            <option value="everything">everything</option>
            <option value="spearman">spearman</option>
            <option value="kendall">kendall</option>
        </param>
        <param label="Maximum RT difference" name="maxt" value="60" type="float"
               help="Maximum difference to calculate RT similarity - values beyond this are assigned zero similarity."/>

                       help="Choose method for normalization of feature intensities.">
                    <option value="none" selected="true">none</option>
                    <option value="TIC">TIC</option>
                    <option value="quantile">quantile</option>
                    <option value="batch.qc">batch.qc</option>
                </param>
                <when value="batch.qc">
                    <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true"
                           help="CSV with sample names (or indices, currently not handled) on rows and columns with:
                           batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
                           ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
                    <param label="QC injection range" name="qc_inj_range" type="integer" value="20"
                             help="How many injections around each injection are to be scanned for presence of QC samples?

                             between 7 and 21. Smaller values provide more local precision but make normalization sensitive
                             to individual poor outliers (though these are first removed using the boxplot function outlier
                             detection), while wider values provide less local precision in normalization but better
                             stability to individual peak areas."/>
                </when>
            </conditional>
        </section>

        <section name="performance" title="Performance">
            <param label="Blocksize" name="blocksize" type="integer" value="2000"

                   help="Definition of experimental design in CSV format." />
        </section>
    </xml>

    <xml name="output_msp">
       <collection label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_collection" type="list">
           <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
           <filter>not msp_output_details['merge_msp']</filter>
       </collection>
       <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp">
           <filter>msp_output_details['merge_msp']</filter>

4:050cfef6ba65

<macros>
    <token name="@TOOL_VERSION@">1.3.0</token>

    <xml name="creator">
        <creator>
            <person
                givenName="Helge"

            <person
                givenName="Martin"
                familyName="Čech"
                url="https://github.com/martenson"
                identifier="0000-0002-9318-1781" />
            <person
                givenName="Zargham"
                familyName="Ahmad"
                url="https://github.com/zargham-ahmad"
                identifier="0000-0002-6096-224X" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI"/>
        </creator>

        <section name="ms_csv" title="Input MS Data as CSV" expanded="true">
            <param label="Input CSV" name="ms" type="data" format="csv"
                   help="Features as columns, rows as samples. Column header in format mz_rt."/>
            <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true"
                   help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/>
            <param label="phenoData" name="csv_phenoData" type="data" format="csv" optional="true"
                   help="Optional csv containing phenoData."/>
        </section>
    </xml>

    <xml name="parameters_xcms">
        <section name="xcms" title="Input MS Data as XCMS" expanded="true">
            <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks"
                   help="Grouped feature data for clustering." />
        </section>
    </xml>

    <xml name="parameters_recetox_aplcms">
        <section name="ms_dataframe" title="Input MS Data as parquet (output from recetox-aplcms)" expanded="true">
            <param label="Input MS1 featureDefinitions" name="ms1_featureDefinitions" type="data" format="parquet"
                   help="Metadata with columns: mz, rt, feature names containing MS data."/>
            <param label="Input MS1 featureValues" name="ms1_featureValues" type="data" format="parquet"
                   help="data with rownames = sample names, colnames = feature names containing MS data."/>
            <param label="phenoData" name="df_phenoData" type="data" format="tsv,csv" optional="true"
                   help="CSV/TSV file containing phenoData (optional)."/>
        </section>
    </xml>

    <xml name="parameters_required">
        <param label="Sigma r" name="sr" type="float" value="0.5" help="Correlational similarity between features."/>
        <param label="Correlation method" name="cor_method" type="select" display="radio"
               help="Choose correlational method to be used - see [1] for details.">
            <option value="pearson" selected="true">pearson</option>
            <option value="spearman">spearman</option>
            <option value="kendall">kendall</option>
        </param>
        <param label="Maximum RT difference" name="maxt" value="60" type="float"
               help="Maximum difference to calculate RT similarity - values beyond this are assigned zero similarity."/>

                       help="Choose method for normalization of feature intensities.">
                    <option value="none" selected="true">none</option>
                    <option value="TIC">TIC</option>
                    <option value="quantile">quantile</option>
                    <option value="batch.qc">batch.qc</option>
                    <option value="qc">qc</option>
                </param>
                <when value="batch.qc">
                    <param label="Metadata details" name="batch_order_qc" type="data" format="csv"
                           help="CSV with sample names (or indices, currently not handled) on rows and columns with:
                           batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
                           ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
                    <param label="QC injection range" name="qc_inj_range" type="integer" value="20"
                             help="How many injections around each injection are to be scanned for presence of QC samples?

                             between 7 and 21. Smaller values provide more local precision but make normalization sensitive
                             to individual poor outliers (though these are first removed using the boxplot function outlier
                             detection), while wider values provide less local precision in normalization but better
                             stability to individual peak areas."/>
                </when>
                <when value="qc">
                    <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true"
                           help="CSV with sample names (or indices, currently not handled) on rows and columns with:
                           batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
                           ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
                    <param label="p.cut" name="p_cut" type="float" value="0.05" 
                            help="Numeric when run order correction is applied, only features showing a run order vs 
                            signal with a linear p-value (after FDR correction) &lt; p.cut will be adjusted.  also requires 
                            r-squared &lt; rsq.cut."/>
                    <param label="rsq.cut" name="rsq_cut" type="float" value="0.1" 
                            help="Numeric when run order correction is applied, only features showing a run order vs signal 
                            with a linear r-squared &gt; rsq.cut will be adjusted. also requires p values &lt; p.cut."/>
                    <param label="p.adjust" name="p_adjust" type="text" value="none" 
                            help="Which p-value adjustment should be used? one of ['holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 
                            'BY', 'fdr', 'none']"/>
                </when>
                <when value="none"/>
                <when value="TIC"/>
                <when value="quantile"/>
            </conditional>
        </section>

        <section name="performance" title="Performance">
            <param label="Blocksize" name="blocksize" type="integer" value="2000"

                   help="Definition of experimental design in CSV format." />
        </section>
    </xml>

    <xml name="output_msp">
       <collection label="Mass spectra from ${tool.name} on ${on_string} list" name="mass_spectra_collection" type="list">
           <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
           <filter>not msp_output_details['merge_msp']</filter>
       </collection>
       <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp">
           <filter>msp_output_details['merge_msp']</filter>