Mercurial > repos > marie-tremblay-metatoul > nmr_alignment
comparison NmrAlignment_xml.xml @ 0:d690c5ad932f draft
planemo upload for repository https://github.com/workflow4metabolomics/nmr_alignment commit 8ddcd37917c778e152d71ff1f0f05a869f8454c2-dirty
author | marie-tremblay-metatoul |
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date | Thu, 24 Nov 2016 12:11:04 -0500 |
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1 <tool id="NmrAlignment" name="NMR_Alignment" version="2016-10-07"> | |
2 | |
3 <description> Alignment of NMR spectra based on the Cluster-based Peak Alignment (CluPA) algorithm </description> | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="3.1.2">R</requirement> | |
7 <requirement type="package" version="1.1_4">r-batch</requirement> | |
8 <requirement type="package" version="1.2.1">r-speaq</requirement> | |
9 </requirements> | |
10 | |
11 <stdio> | |
12 <exit_code range="1:" level="fatal" /> | |
13 </stdio> | |
14 | |
15 <command> | |
16 ## Wrapper | |
17 Rscript $__tool_directory__/NmrAlignment_wrapper.R | |
18 | |
19 ## File input | |
20 #if $inputs.input == "lib": | |
21 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library | |
22 #elif $inputs.input == "zip_file": | |
23 zipfile $inputs.zip_file | |
24 #end if | |
25 | |
26 ## Spectra borders | |
27 left_border $left_border | |
28 right_border $right_border | |
29 | |
30 | |
31 ## Exclusion zone | |
32 zone_exclusion_choices.choice ${zone_exclusion_choices.choice} | |
33 #if str($zone_exclusion_choices.choice) == 'yes': | |
34 #for $i in $zone_exclusion_choices.conditions: | |
35 zone_exclusion_left ${i.zone_exclusion_left} | |
36 zone_exclusion_right ${i.zone_exclusion_right} | |
37 #end for | |
38 #end if | |
39 | |
40 ## Reference spectrum | |
41 reference $reference | |
42 | |
43 ## Segment size | |
44 nDivRange $nDivRange | |
45 | |
46 ## Intensity threshold | |
47 baselineThresh $baselineThresh | |
48 | |
49 ## Outputs | |
50 logOut $logOut | |
51 alignedSpectra $alignedSpectra | |
52 graphOut $graphOut | |
53 </command> | |
54 | |
55 <inputs> | |
56 <conditional name="inputs"> | |
57 <param name="input" type="select" label="Choose your inputs method" > | |
58 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> | |
59 <option value="lib" >Library directory name</option> | |
60 </param> | |
61 <when value="zip_file"> | |
62 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> | |
63 </when> | |
64 <when value="lib"> | |
65 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > | |
66 <validator type="empty_field"/> | |
67 </param> | |
68 </when> | |
69 </conditional> | |
70 | |
71 <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/> | |
72 <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/> | |
73 | |
74 <conditional name="zone_exclusion_choices"> | |
75 <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" > | |
76 <option value="yes" > yes </option> | |
77 <option value="no" selected="true"> no </option> | |
78 </param> | |
79 <when value="yes"> | |
80 <repeat name="conditions" title="exclusion zones"> | |
81 <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" /> | |
82 <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" /> | |
83 </repeat> | |
84 </when> | |
85 <when value="no" /> | |
86 </conditional> | |
87 | |
88 <param name="reference" type="integer" value="0" help="Number of the reference spectrum. Default value is 0: automatic determination of the reference spectrum" /> | |
89 | |
90 <param name="nDivRange" type="integer" value="64" help="Size of a single small segment after division of spectra. Default value is 64" /> | |
91 | |
92 <param name="baselineThresh" type="integer" value="1" help="Threshold to remove all peaks with intensity lower this value. Default value is 1" /> | |
93 | |
94 </inputs> | |
95 | |
96 <outputs> | |
97 <data format="txt" name="logOut" label="${tool.name}_log" /> | |
98 <data format="tabular" name="alignedSpectra" label="${tool.name}_alignedSpectra" /> | |
99 <data format="pdf" name="graphOut" label="${tool.name}_graph" /> | |
100 </outputs> | |
101 | |
102 <help> | |
103 | |
104 .. class:: infomark | |
105 | |
106 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) | |
107 | |
108 .. class:: infomark | |
109 | |
110 **Please cite** | |
111 | |
112 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 | |
113 | |
114 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) | |
115 | |
116 ============= | |
117 NMR Alignment | |
118 ============= | |
119 | |
120 ----------- | |
121 Description | |
122 ----------- | |
123 | |
124 Nuclear Magnetic Resonance Spectrum Alignment based on the Cluster-based Peak Alignment (CluPA) algorithm from the R 'speak' package | |
125 | |
126 ----------------- | |
127 Workflow position | |
128 ----------------- | |
129 | |
130 **Upstream tools** | |
131 | |
132 ========================= ================= ======= | |
133 Name output file format | |
134 ========================= ================= ======= | |
135 NA NA NA | |
136 ========================= ================= ======= | |
137 | |
138 | |
139 **Downstream tools** | |
140 | |
141 +---------------------------+----------------------+--------+ | |
142 | Name | Output file | Format | | |
143 +===========================+======================+========+ | |
144 |NmrBucketing | dataMatrix.tsv | Tabular| | |
145 +---------------------------+----------------------+--------+ | |
146 | | sampleMetadata.tsv | Tabular| | |
147 +---------------------------+----------------------+--------+ | |
148 | | variableMetadata.tsv | Tabular| | |
149 +---------------------------+----------------------+--------+ | |
150 |NmrNormalization | dataMatrix.tsv | Tabular| | |
151 +---------------------------+----------------------+--------+ | |
152 | | sampleMetadata.tsv | Tabular| | |
153 +---------------------------+----------------------+--------+ | |
154 | | variableMetadata.tsv | Tabular| | |
155 +---------------------------+----------------------+--------+ | |
156 |Univariate | variableMetadata.tsv | Tabular| | |
157 +---------------------------+----------------------+--------+ | |
158 |Multivariate | sampleMetadata.tsv | Tabular| | |
159 +---------------------------+----------------------+--------+ | |
160 | | variableMetadata.tsv | Tabular| | |
161 +---------------------------+----------------------+--------+ | |
162 | |
163 | |
164 ----------- | |
165 Input files | |
166 ----------- | |
167 | |
168 +---------------------------+------------+ | |
169 | Parameter : num + label | Format | | |
170 +===========================+============+ | |
171 | 1 : Choose your inputs | zip | | |
172 +---------------------------+------------+ | |
173 | |
174 **Choose your inputs** | |
175 | |
176 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). | |
177 | |
178 | |
179 ---------- | |
180 Parameters | |
181 ---------- | |
182 | |
183 Bucket width | |
184 | size of windows | |
185 | | |
186 | |
187 Left limit | |
188 | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm | |
189 | | |
190 | |
191 Right limit | |
192 | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm | |
193 | | |
194 | |
195 Exclusion zone(s) | |
196 | Spectral regions to exclude, water, solvents, ... resonance | |
197 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible, | |
198 | If NO: no zone to exclude | |
199 | Default value is NO | |
200 | | |
201 | |
202 Left exclusion zone | |
203 | Upper boundary of exclusion zone | |
204 | | |
205 | |
206 Right exclusion zone | |
207 | Lower boundary of exclusion zone | |
208 | |
209 | *Notes:* | |
210 | - these parameters can be used several times using the "Add new exclusion zones" button | |
211 | | |
212 | |
213 Reference spectrum | |
214 | spectrum to which other spectra are aligned | |
215 | Default value is 0: heuristic strategy to find the optimal template developped in the speaq package | |
216 | | |
217 | |
218 Segment size | |
219 | Size of a single small segment after division of spectra | |
220 | Default value: 64 (minimal value adviced) | |
221 | | |
222 | |
223 Intensity threshold | |
224 | All peaks with an intensity below this threshold are removed | |
225 | Default value: 1 | |
226 | | |
227 | |
228 | |
229 ------------ | |
230 Output files | |
231 ------------ | |
232 | |
233 alignedSpectra.tsv | |
234 | tabular output | |
235 | Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities | |
236 | | |
237 | |
238 graphOut.pdf | |
239 | pdf output | |
240 | 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 | |
241 | |
242 | |
243 --------------------------------------------------- | |
244 | |
245 --------------- | |
246 Example | |
247 --------------- | |
248 | |
249 | |
250 .. image:: ./static/images/NmrAlignment.png | |
251 :width: 500 | |
252 | |
253 </help> | |
254 <citations> | |
255 <citation type="doi">10.1093/bioinformatics/btu813</citation> | |
256 </citations> | |
257 | |
258 </tool> |