view nmr_alignement/NmrAlignment_xml.xml @ 2:908e1345d7ca draft

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<tool id="NmrAlignment" name="NMR spectra alignment" version="2.0.2">
	<description>based on the Cluster-based Peak Alignment (CluPA) algorithm</description>
	 <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
	    <requirement type="package" version="1.1_4">r-batch</requirement>
	    <requirement type="package" version="1.2.1">r-speaq</requirement>
  	</requirements>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
  	<command>
		## Wrapper
        Rscript '$__tool_directory__/NmrAlignment_wrapper.R'

		## File input
        #if $inputs.input == "lib":
            library '$__app__.config.user_library_import_dir/$__user_email__/$inputs.library'
		#elif $inputs.input == "tsv_file":
            tsvfile $inputs.tsv_file
        #elif $inputs.input == "zip_file":
            zipfile '$inputs.zip_file'
        #end if

		## Spectra borders
		left_border $left_border
		right_border $right_border

		## Exclusion zone
		zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
		#if str($zone_exclusion_choices.choice) == 'yes':
			#for $i in $zone_exclusion_choices.conditions:
				zone_exclusion_left ${i.zone_exclusion_left}
				zone_exclusion_right ${i.zone_exclusion_right}
			#end for
		#end if

		## Reference spectrum
		reference $reference

		## Segment size
		nDivRange $nDivRange

		## Intensity threshold
		baselineThresh $baselineThresh

		## Outputs
		logOut '$logOut'
		alignedSpectra '$alignedSpectra'
		graphOut '$graphOut'
	</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 Bruker directories</option>
                <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>
                <option value="lib" >Library directory name</option>
            </param>
            <when value="zip_file">
                <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
            </when>
            <when value="tsv_file">
                <param name="tsv_file" type="data" format="tabular" label="Tsv 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="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>
		<param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>

		<conditional name="zone_exclusion_choices">
			<param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
				<option value="yes" > yes </option>
				<option value="no" selected="true"> no </option>
			</param>
			<when value="yes">
				<repeat name="conditions" title="exclusion zones">
					<param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
					<param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
				</repeat>
			</when>
      <when value="no" />
		</conditional>
		<param name="reference" type="integer" value="0" help="Number of the reference spectrum. Default value is 0: automatic determination of the reference spectrum" />
		<param name="nDivRange" type="integer" value="64" help="Size of a single small segment after division of spectra. Default value is 64" />
		<param name="baselineThresh" type="integer" value="1" help="Threshold to remove all peaks with intensity lower this value. Default value is 1" />
	</inputs>

	<outputs>
		<data format="txt" name="logOut" label="${tool.name}_log" />
		<data format="tabular" name="alignedSpectra" label="${tool.name}_alignedSpectra" />
		<data format="pdf" name="graphOut" label="${tool.name}_graph" />
	</outputs>

	<help>

.. class:: infomark

**Authors** Marie Tremblay-Franco ([e-mail])

.. class:: infomark

**Please cite**

T.N. Vu, D. Valkenborg, K. Smets, K.A. Verwaest, R. Dommisse, F. Lemière, A. Verschoren, B. Goethals and K. Laukens. An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics 2011, 12:405. DOI: 10.1186/1471-2105-12-405

T.N. Vu, K. Laukens and D. Valkenborg. A practical experiment of using speaq package. 2015 (https://cran.r-project.org/web/packages/speaq/vignettes/speaq.pdf)

=============
NMR Alignment
=============

-----------
Description
-----------

Nuclear Magnetic Resonance Spectrum Alignment based on the Cluster-based Peak Alignment (CluPA) algorithm from the R 'speak' package

-----------------
Workflow position
-----------------

**Upstream tools**

========================= ================= =======
Name                      output file       format
========================= ================= =======
NA                        NA                NA
========================= ================= =======


**Downstream tools**

+---------------------------+----------------------+--------+
| Name                      | Output file          | Format |
+===========================+======================+========+
|NmrBucketing               | dataMatrix.tsv       | Tabular|
+---------------------------+----------------------+--------+
|                           | sampleMetadata.tsv   | Tabular|
+---------------------------+----------------------+--------+
|                           | variableMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+
|NmrNormalization           | dataMatrix.tsv       | Tabular|
+---------------------------+----------------------+--------+
|                           | sampleMetadata.tsv   | Tabular|
+---------------------------+----------------------+--------+
|                           | variableMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+
|Univariate                 | variableMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+
|Multivariate               | sampleMetadata.tsv   | Tabular|
+---------------------------+----------------------+--------+
|                           | variableMetadata.tsv | Tabular|
+---------------------------+----------------------+--------+


-----------
Input files
-----------

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| 1 : Choose your inputs    |   zip      |
+---------------------------+------------+

**Choose your inputs**

    | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).


----------
Parameters
----------

Bucket width
	| size of windows
	|

Left limit
	| Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm
	|

Right limit
	| Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm
	|

Exclusion zone(s)
	| Spectral regions to exclude, water, solvents, ... resonance
	| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
	| If NO: no zone to exclude
	| Default value is NO
	|

Left exclusion zone
	| Upper boundary of exclusion zone
	|

Right exclusion zone
	| Lower boundary of exclusion zone

| *Notes:*
| - these parameters can be used several times using the "Add new exclusion zones" button
|

Reference spectrum
	| spectrum to which other spectra are aligned
	| Default value is 0: heuristic strategy to find the optimal template developped in the speaq package
	|

Segment size
	| Size of a single small segment after division of spectra
	| Default value: 64 (minimal value adviced)
	|

Intensity threshold
	| All peaks with an intensity below this threshold are removed
	| Default value: 1
	|


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

alignedSpectra.tsv
	| tabular output
	| Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities
	|

graphOut.pdf
	| pdf output
	| Graphical chart of raw and aligned data: whole spectral width, "zoomed" zones depending on the exclusion zones, spectral zone between 2.8 and 2.4ppm corresponding to the citric acid


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

---------------
Example
---------------


.. image:: ./static/images/NmrAlignment.png
        :width: 500

   </help>
   <citations>
       <citation type="doi">10.1093/bioinformatics/btu813</citation>
   </citations>
</tool>