comparison msnbase_readmsdata.xml @ 6:32c20be7002f draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9

5:2a69f9923a70

                <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
--------------

6:32c20be7002f

                <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
--------------