comparison msstatstmt.xml @ 6:f7d8566c18e9 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 86de2cd327423c44d042f98108dc93a8f83982d0

5:439418d3eb81

<tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.0</token>
        <token name="@GALAXY_VERSION@">0</token>
        <xml name="input_options_shared">
            <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." />
            <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." />
            <param name="rmPSM_withfewMea_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove PSM with few measurements within run" help="Only for 'Remove PSM with missing value within run = No'. Yes (default) will remove the features that have 1 or 2 measurements within each run." />
            <param name="rmProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with one feature" help="Yes will remove the proteins which have only 1 peptide and charge. Default is No." />

]]>
    </help>

    <citations>
        <citation type="doi">10.1074/mcp.ra120.002105</citation>
    </citations>
</tool>

6:f7d8566c18e9

<tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <xml name="input_options_shared">
            <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." />
            <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." />
            <param name="rmPSM_withfewMea_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove PSM with few measurements within run" help="Only for 'Remove PSM with missing value within run = No'. Yes (default) will remove the features that have 1 or 2 measurements within each run." />
            <param name="rmProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with one feature" help="Yes will remove the proteins which have only 1 peptide and charge. Default is No." />

]]>
    </help>

    <citations>
        <citation type="doi">10.1074/mcp.ra120.002105</citation>
        <citation type="doi">10.1021/acs.jproteome.2c00051</citation>
    </citations>
</tool>