Mercurial > repos > melpetera > batchcorrection
comparison BC/determine_bc.xml @ 4:23314e1192d4 draft default tip
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author | melpetera |
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date | Thu, 14 Jan 2021 09:56:58 +0000 |
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3:73892ef177e3 | 4:23314e1192d4 |
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1 <tool id="Determine_BC" name="Determine_batch_correction" version="3.0.0"> | |
2 <description>to choose between linear, lowess and loess methods</description> | |
3 | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 | |
8 <requirements> | |
9 <requirement type="package" version="1.1_4">r-batch</requirement> | |
10 <requirement type="package" version="1.7_8">r-ade4</requirement> | |
11 <requirement type="package" version="1.70.0">bioconductor-pcamethods</requirement> | |
12 </requirements> | |
13 | |
14 <stdio> | |
15 <exit_code range="1:" level="fatal" /> | |
16 </stdio> | |
17 | |
18 <command><![CDATA[ | |
19 Rscript $__tool_directory__/batch_correction_3Lwrapper.R | |
20 analyse "determine_bc" | |
21 sampleMetadata "$sampleMetadata" | |
22 dataMatrix "$dataMatrix" | |
23 ref_factor "$ref_factor" | |
24 #if str($advance.option ) == 'show': | |
25 span $advance.span | |
26 #else: | |
27 span "none" | |
28 #end if | |
29 out_graph_pdf "$out_graph_pdf" | |
30 out_preNormSummary "$out_preNormSummary" | |
31 @SM_CUSTOM@ | |
32 ]]></command> | |
33 | |
34 <inputs> | |
35 <param name="dataMatrix" type="data" label="Data matrix file " help="" format="tabular" /> | |
36 <param name="sampleMetadata" type="data" label="Sample metadata file " help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'" format="tabular" /> | |
37 <expand macro="sm_customisation"/> | |
38 <expand macro="foi"/> | |
39 <conditional name="advance"> | |
40 <param name="option" type="select" label="Advanced options" help="should only be put at 'show' if you have good understanding of the span parameter and are willing to adjust it"> | |
41 <option value="show">show</option> | |
42 <option value="hide" selected="true">hide</option> | |
43 </param> | |
44 <when value="show"> | |
45 <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/> | |
46 </when> | |
47 <when value="hide"/> | |
48 </conditional> | |
49 </inputs> | |
50 | |
51 <outputs> | |
52 <data name="out_graph_pdf" label="Determine_BC_graph" format="pdf" ></data> | |
53 <data name="out_preNormSummary" label="Determine_BC_preNormSummary" format="tabular" ></data> | |
54 </outputs> | |
55 | |
56 <tests> | |
57 <test> | |
58 <param name="dataMatrix" value="input-determinebc-dataMatrix.tsv"/> | |
59 <param name="sampleMetadata" value="input-determinebc-sampleMetadata.tsv"/> | |
60 <param name="ref_factor" value="batch"/> | |
61 <param name="option" value="hide"/> | |
62 <param name="span" value="none"/> | |
63 <output name="out_preNormSummary" file="output-determinebc-preNormSummary.txt"/> | |
64 </test> | |
65 </tests> | |
66 | |
67 <help> | |
68 | |
69 .. class:: infomark | |
70 | |
71 **Authors** | |
72 | Jean-Francois Martin - PF MetaToul-AXIOM ; INRAE ; MetaboHUB (for original version of this tool and overall development of the R script) | |
73 | |
74 .. class:: infomark | |
75 | |
76 **Contributors** | |
77 | Melanie Petera - PFEM ; INRAE ; MetaboHUB (for R wrapper and R script improvement) | |
78 | |
79 .. class:: infomark | |
80 | |
81 **Wrapping** | |
82 | Marion Landi - FLAME ; PFEM (for original xml interface and R wrapper) | |
83 | Franck Giacomoni - PFEM ; INRAE ; MetaboHUB (for original xml interface and R wrapper) | |
84 | |
85 --------------------------------------------------- | |
86 | |
87 .. class:: infomark | |
88 | |
89 **Please cite** If you use this tool, please cite: | |
90 | `F.M. van der Kloet, I. Bobeldijk, E.R. Verheij, R.H. Jellema. (2009). "Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping." Journal of Proteome Research p5132-5141 <http://www.ncbi.nlm.nih.gov/pubmed/19754161>`_ | |
91 | |
92 --------------------------------------------------- | |
93 | |
94 ========================== | |
95 Determine_batch_correction | |
96 ========================== | |
97 | |
98 | | |
99 | |
100 ----------- | |
101 Description | |
102 ----------- | |
103 | |
104 | | |
105 | |
106 Generates outputs to help to determine what type of regression to use between linear or non-linear (lowess or loess) functions for batch correction | |
107 using quality control pooled samples (QC-pools) with correction algorithm as described by Van Der Kloet (J Prot Res 2009). | |
108 | |
109 | |
110 Warning: this module does *not* deliver which choice should be made in model type; | |
111 it only provides information to help users in determining which choice may be appropriate, based on their own expertise. | |
112 | |
113 | |
114 This tool is meant to be used prior to the Batch_correction tool to help to make a choice in parameters, | |
115 but it is not a requirement and thus can be avoided. | |
116 | |
117 | | |
118 | |
119 ----------------- | |
120 Workflow position | |
121 ----------------- | |
122 | |
123 .. image:: determine_batch_correction.png | |
124 :width: 600 | |
125 | |
126 | |
127 ----------- | |
128 Input files | |
129 ----------- | |
130 | |
131 +--------------------------+-----------+ | |
132 | Parameter : num + label | Format | | |
133 +==========================+===========+ | |
134 | 1 : Data matrix file | tabular | | |
135 +--------------------------+-----------+ | |
136 | 2 : Sample metadata file | tabular | | |
137 +--------------------------+-----------+ | |
138 | |
139 | | |
140 | |
141 The data matrix file must contain the intensity values of variables. | |
142 | First line must contain all the samples' names. | |
143 | First column must contain all the variables' ID. | |
144 | |
145 | |
146 The sample metadata file must contain at least the three following columns: | |
147 | - a batch column (default to "*batch*") to identify the batches of analyses | |
148 | - an injection order column (default to "*injectionOrder*") composed of integers defining the injection order of samples | |
149 | - a sample type column (default to "*sampleType*") indicating if a sample is a biological one ("*sample*"), a QC-pool ("*pool*") or a blank ("*blank*") | |
150 | *Default values* can be changed according to your data coding using the customisation parameters in the "**Sample metadata file coding parameters**" section. | |
151 | |
152 | |
153 **Notes concerning your design:** | |
154 | - the 3 mandatory columns must not contain NA | |
155 | - your data should contain at least 3 QC-pools in each batch for intra-batch **linear** adjustment and 8 for **lo(w)ess** adjustment | |
156 | |
157 | |
158 | |
159 ---------- | |
160 Parameters | |
161 ---------- | |
162 | |
163 Sample metadata file coding parameters | |
164 | Enables to give the names of columns in the sample metadata table that contain the injection order, the batches and the sample types. | |
165 | Also enables to specify the sample type coding used in the sampletype column. | |
166 | | |
167 | |
168 Factor of interest | |
169 | Name of the factor (column header) that will be used as a categorical variable for design plots (often a biological factor ; if none, put the batch column name). | |
170 | This factor does not affect correction calculation. | |
171 | | |
172 | |
173 Advanced options | |
174 | Should only be put at "show" if you have good understanding of the span parameter and are willing to adjust it. | |
175 | | |
176 | |
177 Span | |
178 | - When advanced option is at "hide" (default): | |
179 | default is 1 for loess regression and is two times the ratio between number of pools and number of samples for lowess regression. | |
180 | - When advanced option is at "show": | |
181 | filled value is used for lowess and loess regressions. | |
182 | |
183 | |
184 ------------ | |
185 Output files | |
186 ------------ | |
187 | |
188 Determine_BC_preNormSummary.tabular | |
189 | tabular output | |
190 | Meaning of results of diagnosis analysis | |
191 | 0 - no preliminary-condition problem | |
192 | 1 - standard deviation of QC-pools or samples = 0 | |
193 | 2 - insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess) | |
194 | 2.5 - less than 2 samples within a batch | |
195 | 3 - significant difference between QC-pools' and samples' means | |
196 | 4 - denominator =0 when on 1 pool per batch non-zero | |
197 | 5 - (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2 | |
198 | 6 - (linear regression only) none of the pool or sample could be corrected if negative and infinite values are turned into NA | |
199 | | |
200 | |
201 Determine_BC_graph.pdf | |
202 | graphical output | |
203 | One page per ion. Plots regression curves for all methods allowed and plot.design results regarding the factor of interest. | |
204 | |
205 | |
206 --------------------------------------------------- | |
207 | |
208 ---------------------- | |
209 Additional information | |
210 ---------------------- | |
211 | |
212 | |
213 .. class:: warningmark | |
214 | |
215 Refer to the corresponding "W4M HowTo" page: | |
216 | `MS data processing - Filters and normalisation <https://download.workflow4metabolomics.org/docs/w4e2018/2018-10_EC_W4E%20-%20Dataprocessing_Filter_and_normalisation.pdf>`_ | |
217 | | |
218 | | |
219 | |
220 | |
221 </help> | |
222 | |
223 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> | |
224 <citations> | |
225 <!-- [HELP] As DOI or BibTex entry --> | |
226 <citation type="doi">10.1021/pr900499r</citation> | |
227 </citations> | |
228 | |
229 | |
230 | |
231 </tool> |