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comparison ReadFids.xml @ 7:122df1bf0a8c draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
author workflow4metabolomics
date Fri, 11 Jul 2025 08:33:38 +0000
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6:6e837e9352a2 7:122df1bf0a8c
1 <tool id="NMR_Read" name="NMR_Read" version="@WRAPPER_VERSION@+galaxy1">
2 <description> Read Bruker NMR raw files</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <required_files>
11 <include path="DrawFunctions.R" />
12 <include path="ReadFids_wrapper.R" />
13 <include path="ReadFids_script.R" />
14 </required_files>
15
16 <command detect_errors="aggressive"><![CDATA[
17 Rscript
18 -e "source('${__tool_directory__}/DrawFunctions.R')"
19 -e "source('${__tool_directory__}/ReadFids_script.R')"
20 -e "source('${__tool_directory__}/ReadFids_wrapper.R')"
21 --fidzipfile "$fidzipfile"
22 --title_line $title_line
23 $subdirectories
24 $dirs_names
25 ]]></command>
26
27 <inputs>
28 <param name="fidzipfile" type="data" format="zip" label="Bruker FID file" />
29 <param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" help="Default value is line 1"/>
30 <param name="subdirectories" label="Presence of subdirectories?" type="boolean" truevalue="--subdirectories" falsevalue="" checked="false" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories"/>
31 <param name="dirs_names" label="Use (sub)directories names as FID names?" type="boolean" truevalue="--dirs_names" falsevalue="" checked="false" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)"/>
32 </inputs>
33
34 <outputs>
35 <data format="tabular" name="dataMatrix" from_work_dir="dataMatrix.tsv" label="${tool.name}_dataMatrix" />
36 <data format="tabular" name="sampleMetadata" from_work_dir="sampleMetadata.tsv" label="${tool.name}_sampleMetadata" />
37 <data format="txt" name="logOut" from_work_dir="logOut.txt" label="${tool.name}_log" />
38 <data format="pdf" name="graphOut" from_work_dir="graphOut.pdf" label="${tool.name}_graph" />
39 </outputs>
40
41
42 <tests>
43 <test>
44 <param name="fidzipfile" location="https://nextcloud.inrae.fr/s/ksGZq9GZfL9R6PD/download/MTBLS1.zip" ftype="zip" />
45 <param name="title_line" value="1" />
46 <param name="subdirectories" value="TRUE" />
47 <param name="dirs_names" value="TRUE" />
48
49 <output name="dataMatrix" location="https://nextcloud.inrae.fr/s/aMs9eM4RwRjeign/download/NMR_ReadFids_dataMatrix.tabular" />
50 <output name="sampleMetadata" value="NMR_ReadFids_sampleMetadata.tabular" />
51 <output name="logOut" value="NMR_ReadFids_log.txt" compare="diff" lines_diff="100" />
52 <output name="graphOut" value="NMR_ReadFids_graph.pdf" compare="diff" lines_diff="100" />
53 </test>
54 </tests>
55
56 <help>
57
58 @HELP_AUTHORS@
59
60
61 =============
62 NMR Read
63 =============
64
65 -----------
66 Description
67 -----------
68
69 Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))
70
71 -----------------
72 Workflow position
73 -----------------
74
75 **Upstream tools**
76
77 ========================= ================= =======
78 Name output file format
79 ========================= ================= =======
80 NA NA NA
81 ========================= ================= =======
82
83
84 **Downstream tools**
85
86 +-----------------------+--------------------------+--------+
87 | Name | Output file | Format |
88 +=======================+==========================+========+
89 |NMR_Preprocessing | dataMatrix | Tabular|
90 +-----------------------+--------------------------+--------+
91 |NMR_Preprocessing | sampleMetadata | Tabular|
92 +-----------------------+--------------------------+--------+
93 |NMR_Preprocessing | NMR_Read_log | TXT |
94 +-----------------------+--------------------------+--------+
95 |NMR_Preprocessing | NMR_Read_graph | PDF |
96 +-----------------------+--------------------------+--------+
97 |NMR_Alignement | dataMatrix | Tabular|
98 +-----------------------+--------------------------+--------+
99 |NMR_Bucketing | dataMatrix | Tabular|
100 +-----------------------+--------------------------+--------+
101 |Normalization | dataMatrix | Tabular|
102 +-----------------------+--------------------------+--------+
103 |Univariate | variableMetadata | Tabular|
104 +-----------------------+--------------------------+--------+
105 |Multivariate | sampleMetadata | Tabular|
106 +-----------------------+--------------------------+--------+
107 | | variableMetadata | Tabular|
108 +-----------------------+--------------------------+--------+
109
110
111 -----------
112 Input files
113 -----------
114
115 +---------------------------+-----------------+
116 | Parameter : num + label | Format |
117 +===========================+=================+
118 | 1 : Choose your inputs | zip |
119 +---------------------------+-----------------+
120
121
122 **Choose your inputs**
123
124 | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.
125
126
127 ----------
128 Parameters
129 ----------
130
131 FID Title line
132 | Line in the acqus file to find the FID title (name)
133 |
134
135 subdirectories
136 | Organization of individual's files
137 | TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
138 |
139
140 dirs_names
141 | Use the (sub)directories names as FID names?
142 |
143
144
145 ------------
146 Output files
147 ------------
148
149 NMR_Read_dataMatrix
150 | tabular output
151 | Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.
152 |
153
154 NMR_Read_sampleMetadata
155 | tabular output
156 | Data matrix with n rows (samples) containing the acquisition parameters for each sample.
157 |
158
159 NMR_Read_log
160 | Text output
161 | Contains warnings
162 |
163
164
165 NMR_Read_graph
166 | pdf output
167 | line plots of FID
168 |
169
170
171 Creating the zip file
172 -----------------------
173
174 .. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows.
175
176 Must contain at least the following files for every sample: fid, acqu and acqus
177
178 .. image:: ./static/images/ReadFids.png
179
180
181
182 **Possible structure and parameters values:**
183
184
185 (1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE
186 (2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE
187 (3) don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE
188 (4) don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE
189
190
191 @HELP_CHANGELOG@
192
193 </help>
194
195 <expand macro="citation" />
196
197 </tool>