Mercurial > repos > melpetera > batchcorrection

comparison BC/determine_bc.xml @ 4:23314e1192d4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author melpetera
date Thu, 14 Jan 2021 09:56:58 +0000
parents
children
comparison
equal deleted inserted replaced
3:73892ef177e3 4:23314e1192d4
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 &lt;http://www.ncbi.nlm.nih.gov/pubmed/19754161&gt;`_
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 &lt;https://download.workflow4metabolomics.org/docs/w4e2018/2018-10_EC_W4E%20-%20Dataprocessing_Filter_and_normalisation.pdf&gt;`_
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>