Mercurial > repos > lecorguille > msnbase_readmsdata
comparison msnbase_readmsdata.xml @ 0:728ebc7ae7dd draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
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date | Tue, 18 Sep 2018 16:04:51 -0400 |
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children | c0a66f15261b |
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1 <tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.0"> | |
2 <description>Imports mass-spectrometry raw data files</description> | |
3 | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 <import>macros_msnbase.xml</import> | |
7 </macros> | |
8 | |
9 <expand macro="requirements"/> | |
10 <expand macro="stdio"/> | |
11 | |
12 <command><![CDATA[ | |
13 @COMMAND_RSCRIPT@/msnbase_readmsdata.r | |
14 | |
15 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): | |
16 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' | |
17 #else | |
18 zipfile '$input' | |
19 #end if | |
20 | |
21 @COMMAND_LOG_EXIT@ | |
22 ]]></command> | |
23 | |
24 <inputs> | |
25 | |
26 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: no_unzip.zip, zip. See the help section below." /> | |
27 | |
28 </inputs> | |
29 | |
30 <outputs> | |
31 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" /> | |
32 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" > | |
33 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> | |
34 </data> | |
35 </outputs> | |
36 | |
37 <tests> | |
38 | |
39 <test> | |
40 <param name="input" value="faahKO_reduce.zip" ftype="zip" /> | |
41 <assert_stdout> | |
42 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> | |
43 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" /> | |
44 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" /> | |
45 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" /> | |
46 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" /> | |
47 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" /> | |
48 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" /> | |
49 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" /> | |
50 </assert_stdout> | |
51 <output name="sampleMetadata" value="sampleMetadata.tsv" /> | |
52 </test> | |
53 <test> | |
54 <param name="input" value="ko15.CDF" ftype="netcdf" /> | |
55 <assert_stdout> | |
56 <has_text text="rowNames: ./ko15.CDF" /> | |
57 <has_text text="ko15.CDF" /> | |
58 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" /> | |
59 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" /> | |
60 <has_text text="./ko15.CDF ko15 ." /> | |
61 </assert_stdout> | |
62 </test> | |
63 <!-- DISABLE FOR TRAVIS | |
64 Useful to generate test-data for the further steps--> | |
65 <test> | |
66 <param name="input" value="ko16.CDF" ftype="netcdf" /> | |
67 <assert_stdout> | |
68 <has_text text="rowNames: ./ko16.CDF" /> | |
69 <has_text text="ko16.CDF" /> | |
70 <has_text text="./ko16.CDF ko16 ." /> | |
71 </assert_stdout> | |
72 </test> | |
73 <test> | |
74 <param name="input" value="wt15.CDF" ftype="netcdf" /> | |
75 <assert_stdout> | |
76 <has_text text="rowNames: ./wt15.CDF" /> | |
77 <has_text text="wt15.CDF" /> | |
78 <has_text text="./wt15.CDF wt15 ." /> | |
79 </assert_stdout> | |
80 </test> | |
81 <test> | |
82 <param name="input" value="wt16.CDF" ftype="netcdf" /> | |
83 <assert_stdout> | |
84 <has_text text="rowNames: ./wt16.CDF" /> | |
85 <has_text text="wt16.CDF" /> | |
86 <has_text text="./wt16.CDF wt16 ." /> | |
87 </assert_stdout> | |
88 </test> | |
89 <!-- --> | |
90 </tests> | |
91 | |
92 <help><![CDATA[ | |
93 | |
94 @HELP_AUTHORS@ | |
95 | |
96 ================== | |
97 MSnbase readMSData | |
98 ================== | |
99 | |
100 ----------- | |
101 Description | |
102 ----------- | |
103 | |
104 Reads as set of XML-based mass-spectrometry data files and | |
105 generates an MSnExp object. This function uses the functionality | |
106 provided by the ‘mzR’ package to access data and meta data in | |
107 ‘mzData’, ‘mzXML’ and ‘mzML’. | |
108 | |
109 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html | |
110 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf | |
111 | |
112 | |
113 ----------------- | |
114 Workflow position | |
115 ----------------- | |
116 | |
117 **Upstream tools** | |
118 | |
119 ========================= ========================================== | |
120 Name Format | |
121 ========================= ========================================== | |
122 Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip | |
123 ========================= ========================================== | |
124 | |
125 The easier way to process is to create a Dataset Collection of the type List | |
126 | |
127 **Downstream tools** | |
128 | |
129 =========================== ==================== ==================== | |
130 Name Output file Format | |
131 =========================== ==================== ==================== | |
132 xcms.findChromPeaks ``*``.raw.RData rdata.msnbase.raw | |
133 =========================== ==================== ==================== | |
134 | |
135 | |
136 | |
137 **Example of a metabolomic workflow** | |
138 | |
139 .. image:: msnbase_readmsdata_workflow.png | |
140 | |
141 --------------------------------------------------- | |
142 | |
143 | |
144 | |
145 ----------- | |
146 Input files | |
147 ----------- | |
148 | |
149 =========================== ================================== | |
150 Parameter : num + label Format | |
151 =========================== ================================== | |
152 OR : Zip file zip | |
153 --------------------------- ---------------------------------- | |
154 OR : Single file mzXML, mzML, mzData, netCDF | |
155 =========================== ================================== | |
156 | |
157 **Choose your inputs** | |
158 | |
159 You have two methods for your inputs: | |
160 | |
161 | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks. | |
162 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). | |
163 | |
164 Zip file: Steps for creating the zip file | |
165 ----------------------------------------- | |
166 | |
167 **Step1: Creating your directory and hierarchize the subdirectories** | |
168 | |
169 | |
170 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip_ software, otherwise your zip will not be well unzipped on the W4M platform (corrupted zip bug). | |
171 | |
172 .. _7Zip: http://www.7-zip.org/ | |
173 | |
174 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild): | |
175 arabidopsis/wild/01.raw | |
176 arabidopsis/mutant/01.raw | |
177 | |
178 **Step2: Creating a zip file** | |
179 | |
180 Create your zip file (*e.g.* arabidopsis.zip). | |
181 | |
182 **Step 3 : Uploading it to our Galaxy server** | |
183 | |
184 If your zip file is less than 2Gb, you can use the Get Data tool to upload it. | |
185 | |
186 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org. | |
187 | |
188 .. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf | |
189 | |
190 For more information, do not hesitate to send us an email at supportATworkflow4metabolomics.org. | |
191 | |
192 Advices for converting your files into mzXML format (XCMS input) | |
193 ---------------------------------------------------------------- | |
194 | |
195 We recommend you to convert your raw files into **mzXML** in centroid mode (smaller files); this way the files will be compatible with the xmcs centWave algorithm. | |
196 | |
197 **We recommend you the following parameters:** | |
198 | |
199 Use Filtering: **True** | |
200 | |
201 Use Peak Picking: **True** | |
202 | |
203 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode | |
204 | |
205 Use zlib: **64** | |
206 | |
207 Binary Encoding: **64** | |
208 | |
209 m/z Encoding: **64** | |
210 | |
211 Intensity Encoding: **64** | |
212 | |
213 | |
214 ------------ | |
215 Output files | |
216 ------------ | |
217 | |
218 xset.RData: rdata.msnbase.raw format | |
219 | |
220 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks". | |
221 | |
222 sampleMetadata.tsv (only when a zip is used) | |
223 | |
224 | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed). | |
225 | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example. | |
226 | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step. | |
227 | |
228 --------------------------------------------------- | |
229 | |
230 Changelog/News | |
231 -------------- | |
232 | |
233 | |
234 **Version 2.4.0.0 - 29/03/2018** | |
235 | |
236 - NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks. | |
237 | |
238 ]]></help> | |
239 | |
240 <expand macro="citation" /> | |
241 </tool> |