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comparison nmr_preprocessing/ReadFids_xml.xml @ 2:7304ec2c9ab7 draft

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author marie-tremblay-metatoul
date Mon, 30 Jul 2018 10:33:03 -0400
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1 <tool id="NMR_Read" name="NMR_Read" version="1.2.0">
2 <description> Read Bruker NMR raw files</description>
3
4 <stdio>
5 <exit_code range="1:" level="fatal" />
6 </stdio>
7
8 <command>
9 ## Wrapper
10 Rscript $__tool_directory__/ReadFids_wrapper.R
11
12 ## File input
13 fidzipfile $fidzipfile
14
15 ## Title line
16 title_line $title_line
17
18 ## Subdirectories
19 subdirectories $subdirectories
20
21 ## Use subdirectories names as FID names?
22 dirs_names $dirs_names
23
24 ## Outputs
25 dataMatrix $dataMatrix
26 sampleMetadata $sampleMetadata
27 logOut $logOut
28 graphOut $graphOut
29
30 </command>
31
32 <inputs>
33 <param name="fidzipfile" type="data" format="no_unzip.zip" label="Bruker FID file" />
34
35 <param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" size="100" help="Default value is line 1"/>
36
37 <param name="subdirectories" label="Presence of subdirectories?" type="select" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories">
38 <option value="FALSE"> FALSE </option>
39 <option value="TRUE"> TRUE </option>
40 </param>
41
42 <param name="dirs_names" label="Use (sub)directories names as FID names?" type="select" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)">
43 <option value="FALSE"> FALSE </option>
44 <option value="TRUE"> TRUE </option>
45 </param>
46 </inputs>
47
48
49
50 <outputs>
51 <data format="tabular" name="dataMatrix" label="${tool.name}_dataMatrix" />
52 <data format="tabular" name="sampleMetadata" label="${tool.name}_sampleMetadata" />
53 <data format="txt" name="logOut" label="${tool.name}_log" />
54 <data format="pdf" name="graphOut" label="${tool.name}_graph" />
55 </outputs>
56
57
58 <tests>
59 <test>
60 <param name="fidzipfile" value="MTBLS1.zip" ftype="zip" />
61 <param name="title_line" value="1" />
62 <param name="subdirectories" value="TRUE" />
63 <param name="dirs_names" value="TRUE" />
64
65 <output name="dataMatrix" value="NMR_ReadFids_dataMatrix.tabular" />
66
67 </test>
68 </tests>
69
70
71
72 <help>
73
74 .. class:: infomark
75
76 **Authors** Manon Martin (manon.martin@uclouvain.be) and Marie Tremblay-Franco (marie.tremblay-franco@inra.fr; Galaxy integration)
77
78 .. class:: infomark
79
80
81 =============
82 NMR Read
83 =============
84
85 -----------
86 Description
87 -----------
88
89 Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))
90
91 -----------------
92 Workflow position
93 -----------------
94
95 **Upstream tools**
96
97 ========================= ================= =======
98 Name output file format
99 ========================= ================= =======
100 NA NA NA
101 ========================= ================= =======
102
103
104 **Downstream tools**
105
106 +-----------------------+--------------------------+--------+
107 | Name | Output file | Format |
108 +=======================+==========================+========+
109 |NMR_Preprocessing | dataMatrix | Tabular|
110 +-----------------------+--------------------------+--------+
111 |NMR_Preprocessing | sampleMetadata | Tabular|
112 +-----------------------+--------------------------+--------+
113 |NMR_Preprocessing | NMR_Read_log | TXT |
114 +-----------------------+--------------------------+--------+
115 |NMR_Preprocessing | NMR_Read_graph | PDF |
116 +-----------------------+--------------------------+--------+
117 |NMR_Alignement | dataMatrix | Tabular|
118 +-----------------------+--------------------------+--------+
119 |NMR_Bucketing | dataMatrix | Tabular|
120 +-----------------------+--------------------------+--------+
121 |Normalization | dataMatrix | Tabular|
122 +-----------------------+--------------------------+--------+
123 |Univariate | variableMetadata | Tabular|
124 +-----------------------+--------------------------+--------+
125 |Multivariate | sampleMetadata | Tabular|
126 +-----------------------+--------------------------+--------+
127 | | variableMetadata | Tabular|
128 +-----------------------+--------------------------+--------+
129
130
131 -----------
132 Input files
133 -----------
134
135 +---------------------------+-----------------+
136 | Parameter : num + label | Format |
137 +===========================+=================+
138 | 1 : Choose your inputs | zip |
139 +---------------------------+-----------------+
140
141
142 **Choose your inputs**
143
144 | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.
145
146
147 ----------
148 Parameters
149 ----------
150
151 FID Title line
152 | Line in the acqus file to find the FID title (name)
153 |
154
155 subdirectories
156 | Organization of individual's files
157 | TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
158 |
159
160 dirs_names
161 | Use the (sub)directories names as FID names?
162 |
163
164
165 ------------
166 Output files
167 ------------
168
169 NMR_Read_dataMatrix
170 | tabular output
171 | Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.
172 |
173
174 NMR_Read_sampleMetadata
175 | tabular output
176 | Data matrix with n rows (samples) containing the acquisition parameters for each sample.
177 |
178
179 NMR_Read_log
180 | Text output
181 | Contains warnings
182 |
183
184
185 NMR_Read_graph
186 | pdf output
187 | line plots of FID
188 |
189
190
191 Creating the zip file
192 -----------------------
193
194 .. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows.
195
196 Must contain at least the following files for every sample: fid, acqu and acqus
197
198 .. image:: ./static/images/ReadFids.png
199 :height: 400
200
201
202
203 **Possible structure and parameters values:**
204
205
206 (1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE
207 (2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE
208 (3) don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE
209 (4) don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE
210
211
212
213 </help>
214
215
216 <citations>
217
218 <citation type="bibtex">@PhDThesis{Rousseau2011,
219 title = {Statistical contribution to the analysis of metabonomics data in $^1$H NMR spectroscopy},
220 author = {Rousseau, R.},
221 school = {Institut de Statistique, Biostatistique et Sciences Actuarielles, Universit{\'e} catholique de Louvain},
222 year = {2011}}
223 </citation>
224
225 </citations>
226
227
228 </tool>