comparison msstatstmt.xml @ 3:5667ff6f7a40 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 6bd1ff7b41dcc9d66523ac005700f9a1ae434afa"

2:782bd55b000b

                            dot.size.profile = $out_plots_opt.adv.dot_size_profile,
                            ncol.guide = $out_plots_opt.adv.ncol_guide,
                            width = $out_plots_opt.width,
                            height = $out_plots_opt.height,
                            #if $out_plots_opt.which_Protein.select != 'list'
                            which.Protein = "$out_plots_opt.which_Protein.select",
                            #else
                            which.Protein = unlist(read.table("$out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
                            #end if
                            originalPlot = $out_plots_opt.adv.originalPlot,
                            summaryPlot = $out_plots_opt.adv.summaryPlot)

        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="input">
            <param name="input_src" type="select" label="Input Source">
                <option value="MSstatsTMT">MStatsTMT (11 column format)</option>
                <option value="MaxQuant">MaxQuant</option>
                <option value="OpenMS">OpenMS</option>
                <option value="PD">Proteome Discoverer</option>
            </param>
            <when value="MSstatsTMT">
                <param name="msstatstmt_input" type="data" format="tabular" label="MStatsTMT (11 column format)"/>
            </when>
            <when value="MaxQuant">
                <param name="evidence" type="data" format="tabular" label="evidence.txt - feature-level data"/>
                <param name="proteinGroups" type="data" format="tabular" label="proteinGroups.txt" help="It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'"/>
                <param name="annotation" type="data" format="tabular" label="annotation.txt" help="Data frame which contains column Run, Fraction, TechRepMixture, Channel, Condition, BioReplicate, Mixture." />

                    <has_text text="PAMI-176_Mouse_A-J_1" />
                    <has_text text="Long_LF" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.

**Notes**

3:5667ff6f7a40

                            dot.size.profile = $out_plots_opt.adv.dot_size_profile,
                            ncol.guide = $out_plots_opt.adv.ncol_guide,
                            width = $out_plots_opt.width,
                            height = $out_plots_opt.height,
                            #if $out_plots_opt.which_Protein.select != 'list'
                            #if $out_plots_opt.which_Protein.select == "allonly" and $plot_type == "ProfilePlot"
                            which.Protein = "all",
                            #else
                            which.Protein = "$out_plots_opt.which_Protein.select",
                            #end if
                            #else
                            which.Protein = unlist(read.table("$out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
                            #end if
                            originalPlot = $out_plots_opt.adv.originalPlot,
                            summaryPlot = $out_plots_opt.adv.summaryPlot)

        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="input">
            <param name="input_src" type="select" label="Input Source">
                <option value="MSstatsTMT">MSstatsTMT (11 column format)</option>
                <option value="MaxQuant">MaxQuant</option>
                <option value="OpenMS">OpenMS</option>
                <option value="PD">Proteome Discoverer</option>
            </param>
            <when value="MSstatsTMT">
                <param name="msstatstmt_input" type="data" format="tabular" label="MSstatsTMT (11 column format)"/>
            </when>
            <when value="MaxQuant">
                <param name="evidence" type="data" format="tabular" label="evidence.txt - feature-level data"/>
                <param name="proteinGroups" type="data" format="tabular" label="proteinGroups.txt" help="It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'"/>
                <param name="annotation" type="data" format="tabular" label="annotation.txt" help="Data frame which contains column Run, Fraction, TechRepMixture, Channel, Condition, BioReplicate, Mixture." />

                    <has_text text="PAMI-176_Mouse_A-J_1" />
                    <has_text text="Long_LF" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="input">
                <param name="input_src" value="MaxQuant"/>
                <param name="evidence" ftype="tabular" value="evidence.txt"/>
                <param name="annotation" ftype="tabular" value="annotation.txt"/>
                <param name="proteinGroups" ftype="tabular" value="proteinGroups.txt"/>
            </conditional>
            <param name="selected_outputs" value="ProfilePlot"/>
            <conditional name="which_Protein">
                <param name="select" value="allonly"/>
            </conditional>
            <output name="out_profile_plot" file="ProfilePlot_allonly.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.

**Notes**