comparison abims_CAMERA_annotateDiffreport.xml @ 17:73d82de36369 draft

planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049

16:a2c49996603e

<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.3">

    <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>

    <macros>
        <import>macros.xml</import>

        nSlaves \${GALAXY_SLOTS:-1}

        ## output
        variableMetadataOutput '$variableMetadata'
        dataMatrixOutput '$datamatrix'

        ## groupFWHM
        sigma $groupfwhm.sigma
        perfwhm $groupfwhm.perfwhm

        <expand macro="input_file_load"/>
    </inputs>

    <outputs>
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
        <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
        <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" >
            <filter>quick_block['quick'] == 'FALSE'</filter>
            <change_format>
                <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
                <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />

            <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <expand macro="test_annotate_quick_true"/>
            <expand macro="test_file_load_zip"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
        </test>-->
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <expand macro="test_annotate_quick_true"/>
            <expand macro="test_file_load_single"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <expand macro="test_annotate_quick_true"/>
            <expand macro="test_file_load_single"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" />
            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <conditional name="quick_block">

                        <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/>
                    </conditional>
                </section>
            </conditional>
            <expand macro="test_file_load_single"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" />
            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" />
        </test>
    </tests>

+---------------------------+---------------------------------------+------------------------------------------------+
| Name                      | Output file                           | Format                                         |
+===========================+=======================================+================================================+
|CAMERA_combinexsAnnot      |xset.annotate.Rdata                    | rdata.camera.positive or rdata.camera.negative |
+---------------------------+---------------------------------------+------------------------------------------------+
|Determine Vdk or Lowess    |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|Normalization Vdk/Lowess   |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|Anova                      |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|PCA                        |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|Hierarchical Clustering    |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+


The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools:

    | Determine Vdk or Lowess
    | Normalization Vdk/Lowess
    | Anova
    | PCA

xset.annotate.variableMetadata.tsv

    | For each metabolite (row) :
    | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup

xset.annotate.dataMatrix.tsv

    | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).

xset.annotate.zip

    | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).

xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative

------

.. class:: infomark

The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:

    | Determine Vdk or Lowess (Data correction)
    | Normalization Vdk/Lowess (Data correction)
    | Anova (Statistical analysis)
    | PCA (Statistical analysis)

Output files
------------

**Example of an xset.annotate.dataMatrix.tsv output**

.. image:: annotatediffreport_dataMatrix.png

**Example of a part of xset.annotate.variableMetadata.tsv output**

.. image:: annotatediffreport_variableMetadata.png


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

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

**Version 2.2.3 - 30/04/2018**

- NEW: support the new xcms 3.0.0 wrapper

**Version 2.2.2 - 01/03/2018**

17:73d82de36369

<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.4">

    <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>

    <macros>
        <import>macros.xml</import>

        nSlaves \${GALAXY_SLOTS:-1}

        ## output
        variableMetadataOutput '$variableMetadata'

        ## groupFWHM
        sigma $groupfwhm.sigma
        perfwhm $groupfwhm.perfwhm

        <expand macro="input_file_load"/>
    </inputs>

    <outputs>
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
        <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" >
            <filter>quick_block['quick'] == 'FALSE'</filter>
            <change_format>
                <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
                <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />

            <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <expand macro="test_annotate_quick_true"/>
            <expand macro="test_file_load_zip"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
        </test>-->
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <expand macro="test_annotate_quick_true"/>
            <expand macro="test_file_load_single"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <expand macro="test_annotate_quick_true"/>
            <expand macro="test_file_load_single"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" lines_diff="2" />
        </test>
        <test>
            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
            <expand macro="test_annotate_diffreport"/>
            <conditional name="quick_block">

                        <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/>
                    </conditional>
                </section>
            </conditional>
            <expand macro="test_file_load_single"/>
            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" lines_diff="2"/>
        </test>
    </tests>

+---------------------------+---------------------------------------+------------------------------------------------+
| Name                      | Output file                           | Format                                         |
+===========================+=======================================+================================================+
|CAMERA_combinexsAnnot      |xset.annotate.Rdata                    | rdata.camera.positive or rdata.camera.negative |
+---------------------------+---------------------------------------+------------------------------------------------+
|Determine Vdk or Lowess    |xset.annotate.variableMetadata.tsv     | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|Normalization Vdk/Lowess   |xset.annotate.variableMetadata.tsv     | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|Anova                      |xset.annotate.variableMetadata.tsv     | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|PCA                        |xset.annotate.variableMetadata.tsv     | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+
|Hierarchical Clustering    |xset.annotate.variableMetadata.tsv     | Tabular                                        |
+---------------------------+---------------------------------------+------------------------------------------------+


The output file **xset.annotate.variableMetadata.tsv** is an tabular file. You can continue your analysis using it in the following tools:

    | Determine Vdk or Lowess
    | Normalization Vdk/Lowess
    | Anova
    | PCA

xset.annotate.variableMetadata.tsv

    | For each metabolite (row) :
    | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup

xset.annotate.zip

    | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).

xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative

------

.. class:: infomark

The output **"xset.annotate.variableMetadata.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:

    | Determine Vdk or Lowess (Data correction)
    | Normalization Vdk/Lowess (Data correction)
    | Anova (Statistical analysis)
    | PCA (Statistical analysis)

Output files
------------

**Example of a part of xset.annotate.variableMetadata.tsv output**

.. image:: annotatediffreport_variableMetadata.png


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

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

**Version 2.2.4 - 09/10/2018**

- NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job

**Version 2.2.3 - 30/04/2018**

- NEW: support the new xcms 3.0.0 wrapper

**Version 2.2.2 - 01/03/2018**