comparison macros.xml @ 1:8a6c7302de66 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit 01a6a2434c6e77b5061ada328d849a4ad7c30529

0:cd2f3a280463

            <param name="count_cell_carrier" type="integer" value="200" min="0" label="Number of cells in the carrier channel" help="What is the number of cells in the carrier channel?"/> 
            <param name="single_cells" type="select" label="Single-cell channels present in the experiment" multiple="true" optional="false" min="1" help="What are the single-cell channels present in the experiment? At least one channel must be selected!">
                <options from_dataset="input_annotations">
                    <column name="name" index="3"/>
                    <column name="value" index="3"/>
                    <filter type="unique_value" name="unique" column="3"/>
                </options>
            </param>
            <param name="SCR_threshold" type="float" value="0.1" min="0" max="1" label="Mean SCR threshold" help="Mean sample-to-carrier (SCR) threshold. 0.1 corresponds to 10%."/> 
            <param name="qvalue_level" type="select" display="radio" label="Filter based on PSM, peptide or protein-level q-values?" help="Whether to perform the q-value computation and filtration on the PSM, peptide or protein level.">
                <option value="PSM">PSM</option>

        <section name="peptide_filtering" title="Peptide filtering" expanded="true">
            <param name="samples_to_keep" type="select" min="1" optional="false" label="Which samples to keep?" multiple="true" help="Which samples to keep? We recommend filtering out Carrier and Unused channels at this step.">
                <options from_dataset="input_annotations">
                    <column name="name" index="3"/>
                    <column name="value" index="3"/>
                    <filter type="unique_value" name="unique" column="3"/>
                </options>
            </param>
            <conditional name="filter_median_intensity">
                <param type="select" name="cut_median_intensity" label="Filter based on median relative intensity?" help="Whether to filter based on median intensity.">
                    <option value="no" selected="true">no</option> 

1:8a6c7302de66

            <param name="count_cell_carrier" type="integer" value="200" min="0" label="Number of cells in the carrier channel" help="What is the number of cells in the carrier channel?"/> 
            <param name="single_cells" type="select" label="Single-cell channels present in the experiment" multiple="true" optional="false" min="1" help="What are the single-cell channels present in the experiment? At least one channel must be selected!">
                <options from_dataset="input_annotations">
                    <column name="name" index="3"/>
                    <column name="value" index="3"/>
                    <filter type="unique_value" column="3"/>
                </options>
            </param>
            <param name="SCR_threshold" type="float" value="0.1" min="0" max="1" label="Mean SCR threshold" help="Mean sample-to-carrier (SCR) threshold. 0.1 corresponds to 10%."/> 
            <param name="qvalue_level" type="select" display="radio" label="Filter based on PSM, peptide or protein-level q-values?" help="Whether to perform the q-value computation and filtration on the PSM, peptide or protein level.">
                <option value="PSM">PSM</option>

        <section name="peptide_filtering" title="Peptide filtering" expanded="true">
            <param name="samples_to_keep" type="select" min="1" optional="false" label="Which samples to keep?" multiple="true" help="Which samples to keep? We recommend filtering out Carrier and Unused channels at this step.">
                <options from_dataset="input_annotations">
                    <column name="name" index="3"/>
                    <column name="value" index="3"/>
                    <filter type="unique_value" column="3"/>
                </options>
            </param>
            <conditional name="filter_median_intensity">
                <param type="select" name="cut_median_intensity" label="Filter based on median relative intensity?" help="Whether to filter based on median intensity.">
                    <option value="no" selected="true">no</option>