diff NmrAlignment_xml.xml @ 0:d690c5ad932f draft

planemo upload for repository https://github.com/workflow4metabolomics/nmr_alignment commit 8ddcd37917c778e152d71ff1f0f05a869f8454c2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NmrAlignment_xml.xml	Thu Nov 24 12:11:04 2016 -0500
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+<tool id="NmrAlignment" name="NMR_Alignment" version="2016-10-07">
+
+	 <description> Alignment of NMR spectra 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 == "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="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="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>