comparison msstats.xml @ 7:de7593c29499 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 63cff07026599f16d57da27c5897b7e88ad41ae5

6:b7034eff0db1

        <xml name="removeProtein_with1Peptide">
            <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
        </xml>
        
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        cat '$msstats_script' > '$r_script' &&

-----

**Input data**

- Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <http://coxdocs.org/doku.php?id=maxquant:start/>`_, `OpenSWATH <http://openswath.org/en/latest/>`_

    - MSstats format: tabular file with 10 column either manually curated or other sources such as Swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive: 
    
        - ProteinName: protein ID or peptide ID for peptide-level modeling and analysis; statistical analysis will be done separately for each unique label in this column
        - PeptideSequence: Amino acid sequence for each peptide. If the peptide sequences should be distinguished based on post-translational modifications, this column can be renamed to PeptideModifiedSequence.

7:de7593c29499

        <xml name="removeProtein_with1Peptide">
            <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
        </xml>
        
    </macros>
    <xrefs>
        <xref type="bio.tools">msstatstmt</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        cat '$msstats_script' > '$r_script' &&

-----

**Input data**

- Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <https://cox-labs.github.io/coxdocs/maxquant_instructions.html>`_, `OpenSWATH <http://openswath.org/en/latest/>`_

    - MSstats format: tabular file with 10 column either manually curated or other sources such as Swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive: 
    
        - ProteinName: protein ID or peptide ID for peptide-level modeling and analysis; statistical analysis will be done separately for each unique label in this column
        - PeptideSequence: Amino acid sequence for each peptide. If the peptide sequences should be distinguished based on post-translational modifications, this column can be renamed to PeptideModifiedSequence.