comparison msnbase_readmsdata.xml @ 10:84533814b1d5 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01

9:3d8a68b45153

            <param name="input" value="faahKO_reduce.zip"  ftype="zip" />
            <assert_stdout>
                <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
                <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
                <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
                <has_text text="faahKO_reduce/KO/ko15.CDF        ko15           KO" />
                <has_text text="faahKO_reduce/KO/ko16.CDF        ko16           KO" />
                <has_text text="faahKO_reduce/WT/wt15.CDF        wt15           WT" />
                <has_text text="faahKO_reduce/WT/wt16.CDF        wt16           WT" />
            </assert_stdout>

            <param name="input" value="ko15.CDF"  ftype="netcdf" />
            <assert_stdout>
                <has_text text="rowNames: ./ko15.CDF" />
                <has_text text="ko15.CDF" />
                <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
                <has_text text="./ko15.CDF        ko15            ." />
            </assert_stdout>
        </test>
        <!-- DISABLE FOR TRAVIS
        Useful to generate test-data for the further steps-->
        <test>
            <param name="input" value="ko16.CDF"  ftype="netcdf" />
            <assert_stdout>
                <has_text text="rowNames: ./ko16.CDF" />
                <has_text text="ko16.CDF" />

                <has_text text="rowNames: ./wt16.CDF" />
                <has_text text="wt16.CDF" />
                <has_text text="./wt16.CDF        wt16            ." />
            </assert_stdout>
        </test>
        <!-- -->
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

Name                        Output file          Format
=========================== ==================== ====================
xcms.findChromPeaks         ``*``.raw.RData      rdata.msnbase.raw
=========================== ==================== ====================

 

**Example of a metabolomic workflow**

.. image:: msnbase_readmsdata_workflow.png

**Choose your inputs**

You have two methods for your inputs:

    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks. 
    | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).

Zip file: Steps for creating the zip file
-----------------------------------------

sampleMetadata.tsv (only when a zip is used)

    | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
    | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
    | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step. 

---------------------------------------------------

Changelog/News
--------------


**Version 2.4.0.0 - 29/03/2018**

- NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.

10:84533814b1d5

            <param name="input" value="faahKO_reduce.zip"  ftype="zip" />
            <assert_stdout>
                <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
                <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
                <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
                <has_text text="faahKO_reduce/KO/ko15.CDF        ko15           KO" />
                <has_text text="faahKO_reduce/KO/ko16.CDF        ko16           KO" />
                <has_text text="faahKO_reduce/WT/wt15.CDF        wt15           WT" />
                <has_text text="faahKO_reduce/WT/wt16.CDF        wt16           WT" />
            </assert_stdout>

            <param name="input" value="ko15.CDF"  ftype="netcdf" />
            <assert_stdout>
                <has_text text="rowNames: ./ko15.CDF" />
                <has_text text="ko15.CDF" />
                <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
                <has_text text="./ko15.CDF        ko15            ." />
            </assert_stdout>
        </test>
        <!-- DISABLE FOR TRAVIS
        Useful to generate test-data for the further steps
        <test>
            <param name="input" value="ko16.CDF"  ftype="netcdf" />
            <assert_stdout>
                <has_text text="rowNames: ./ko16.CDF" />
                <has_text text="ko16.CDF" />

                <has_text text="rowNames: ./wt16.CDF" />
                <has_text text="wt16.CDF" />
                <has_text text="./wt16.CDF        wt16            ." />
            </assert_stdout>
        </test>
        -->
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

Name                        Output file          Format
=========================== ==================== ====================
xcms.findChromPeaks         ``*``.raw.RData      rdata.msnbase.raw
=========================== ==================== ====================



**Example of a metabolomic workflow**

.. image:: msnbase_readmsdata_workflow.png

**Choose your inputs**

You have two methods for your inputs:

    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks.
    | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).

Zip file: Steps for creating the zip file
-----------------------------------------

sampleMetadata.tsv (only when a zip is used)

    | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
    | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
    | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step.

---------------------------------------------------

Changelog/News
--------------

.. _News: https://bioconductor.org/packages/release/bioc/news/MSnbase/NEWS

**Version 2.8.2.0 - 08/04/2019**

- UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.

**Version 2.4.0.0 - 29/03/2018**

- NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.