comparison abims_xcms_xcmsSet.xml @ 15:1a9bbd4670e8 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94

14:7c19176e1929

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.9">
    
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
    
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>
    
    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":

        xsetRdataOutput $xsetRData
        sampleMetadataOutput $sampleMetadata
        ticspdf $ticsRawPdf
        bicspdf $bpcsRawPdf

        ## profmethod $profmethod 
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
            #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
            #end if 
            #if $methods.options_c.option == "show":
                mzdiff $methods.options_c.mzdiff
                snthresh $methods.options_c.snthresh
                integrate $methods.options_c.integrate
                noise $methods.options_c.noise

            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        @COMMAND_LOG_EXIT@
    ]]></command>
    
    <inputs>

        <conditional name="inputs">
            <param name="input" type="select" label="Choose your inputs method" >
                <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>

            <when value="zip_file">
                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
             </when>
            <when value="lib">
                <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
                <validator type="empty_field"/> 
            </param>
                </when>

        </conditional>

       
<!--
        <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
            <option value="bin" selected="true">bin</option>
            <option value="binlin">binlin</option>
            <option value="binlinbase">binlinbase</option>

                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
                        <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
                            <validator type="empty_field"/> 
                        </param>
                    </when>
                    <when value="hide">
                    </when>
                </conditional>
                        
                <conditional name="options_c">
                    <param name="option" type="select" label="Advanced options" >
                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>

                <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
                <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
        <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
        <data name="ticsRawPdf"   format="pdf" label="xset.TICs_raw.pdf" />
        <data name="bpcsRawPdf"   format="pdf" label="xset.BPCs_raw.pdf" />
        <data name="log" format="txt" label="xset.log.txt" />
    </outputs>
    
    <tests>
        <!--<test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
            <param name="methods|method" value="matchedFilter" />

                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[

@HELP_AUTHORS@

============

**Upstream tools**

========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                zip     NA       
========================= ================= ======= =========


**Downstream tools**

.. image:: XCMS_Galaxy_workflow.png


------

.. class:: infomark 

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

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

Extraction method for peaks detection
-------------------------------------

**Matched Filter**

    | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. 
    | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).


**cent Wave**

    | This file is necessary in the Anova and PCA step of the workflow.

xset.RData: rdata.xcms.raw format

    | Rdata file that is necessary in the second step of the workflow "xcms.group".
    
------

.. class:: infomark 

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

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

Parameters
----------

    | Method -> **matchedFilter**
    | step   -> **0.01**
    | fwhm   -> **4** 
    | Advanced option -> **show**
    | max: -> **50**
    | snthresh -> **1**
    | steps -> **2**

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

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

**Version 2.0.9 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0

**Version 2.0.8 - 06/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies

15:1a9bbd4670e8

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.10">

    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>

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

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":

        xsetRdataOutput $xsetRData
        sampleMetadataOutput $sampleMetadata
        ticspdf $ticsRawPdf
        bicspdf $bpcsRawPdf

        ## profmethod $profmethod
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
            #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
            #end if
            #if $methods.options_c.option == "show":
                mzdiff $methods.options_c.mzdiff
                snthresh $methods.options_c.snthresh
                integrate $methods.options_c.integrate
                noise $methods.options_c.noise

            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        @COMMAND_LOG_EXIT@
    ]]></command>

    <inputs>

        <conditional name="inputs">
            <param name="input" type="select" label="Choose your inputs method" >
                <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>

            <when value="zip_file">
                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
             </when>
            <when value="lib">
                <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
                <validator type="empty_field"/>
            </param>
                </when>

        </conditional>


<!--
        <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
            <option value="bin" selected="true">bin</option>
            <option value="binlin">binlin</option>
            <option value="binlinbase">binlinbase</option>

                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>
                    <when value="show">
                        <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
                            <validator type="empty_field"/>
                        </param>
                    </when>
                    <when value="hide">
                    </when>
                </conditional>

                <conditional name="options_c">
                    <param name="option" type="select" label="Advanced options" >
                        <option value="show">show</option>
                        <option value="hide" selected="true">hide</option>
                    </param>

                <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
                <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
        <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
        <data name="ticsRawPdf"   format="pdf" label="xset.TICs_raw.pdf" />
        <data name="bpcsRawPdf"   format="pdf" label="xset.BPCs_raw.pdf" />
        <data name="log" format="txt" label="xset.log.txt" />
    </outputs>

    <tests>
        <!--<test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
            <param name="methods|method" value="matchedFilter" />

                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

============

**Upstream tools**

========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                zip     NA
========================= ================= ======= =========


**Downstream tools**

.. image:: XCMS_Galaxy_workflow.png


------

.. class:: infomark

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

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

Extraction method for peaks detection
-------------------------------------

**Matched Filter**

    | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
    | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).


**cent Wave**

    | This file is necessary in the Anova and PCA step of the workflow.

xset.RData: rdata.xcms.raw format

    | Rdata file that is necessary in the second step of the workflow "xcms.group".

------

.. class:: infomark

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

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

Parameters
----------

    | Method -> **matchedFilter**
    | step   -> **0.01**
    | fwhm   -> **4**
    | Advanced option -> **show**
    | max: -> **50**
    | snthresh -> **1**
    | steps -> **2**

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

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

**Version 2.0.10 - 22/12/2016**

- BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph

**Version 2.0.9 - 06/07/2016**

- UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0

**Version 2.0.8 - 06/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies