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author workflow4metabolomics
date Fri, 26 Jul 2019 16:49:18 -0400
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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.5">
2
3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements"/>
10 <expand macro="stdio"/>
11
12 <command><![CDATA[
13 @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r
14 image_pos '$image_pos'
15 image_neg '$image_neg'
16
17 pos $pos tol
18 $tol ruleset
19 $ruleset keep_meta
20 $keep_meta
21
22 convertRTMinute $export.convertRTMinute
23 numDigitsMZ $export.numDigitsMZ
24 numDigitsRT $export.numDigitsRT
25
26 ]]></command>
27
28 <inputs>
29 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
30 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
31
32 <param name="pos" type="select" label="Returned peaklist polarity mode">
33 <option value="TRUE" selected="true">positive</option>
34 <option value="FALSE" >negative</option>
35 </param>
36
37 <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
38 <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
39 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
40
41 <section name="export" title="Export options">
42 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
43 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
44 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
45 </section>
46 </inputs>
47
48 <outputs>
49 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
50 <!--
51 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" from_work_dir="combinexsAnnos.RData" />
52 -->
53 </outputs>
54
55 <tests>
56 <test>
57 <!-- TODO: generer des vrais dataset pos et neg-->
58 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
59 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
60 <param name="pos" value="TRUE"/>
61 <param name="tol" value="2"/>
62 <param name="ruleset" value="1,1"/>
63 <section name="export">
64 <param name="convertRTMinute" value="True"/>
65 <param name="numDigitsMZ" value="4" />
66 <param name="numDigitsRT" value="1" />
67 </section>
68 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
69 </test>
70 </tests>
71
72
73 <help><![CDATA[
74
75 @HELP_AUTHORS@
76
77 =======================
78 Xcms.combinexsAnnos
79 =======================
80
81 -----------
82 Description
83 -----------
84
85 **What it does?**
86
87 This function check annotations of ion species with the help of a sample from opposite ion mode.
88 As first step it searches for pseudospectra from the positive and the negative sample within a reten-
89 tion time window. For every result the m/z differences between both samples are matched against
90 specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H
91 with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are
92 changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion
93 mode with recalculated annotations.
94
95 **Details**
96
97 Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno-
98 tation the resulting peaklist only includes annotation with matches peaks from both mode according
99 to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is
100 a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.
101 A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and
102 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!
103
104
105
106 -----------------
107 Workflow position
108 -----------------
109
110
111 **Upstream tools**
112
113 ========================= ======================= ===================== ==========
114 Name Output file Format Parameter
115 ========================= ======================= ===================== ==========
116 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file
117 ------------------------- ----------------------- --------------------- ----------
118 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file
119 ========================= ======================= ===================== ==========
120
121 **Downstream tools**
122
123 +---------------------------+-----------------------------------------+--------+
124 | Name | Output file | Format |
125 +===========================+=========================================+========+
126 |Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
127 +---------------------------+-----------------------------------------+--------+
128 |Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
129 +---------------------------+-----------------------------------------+--------+
130 |Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
131 +---------------------------+-----------------------------------------+--------+
132 |Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
133 +---------------------------+-----------------------------------------+--------+
134
135
136
137 The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools:
138 | Batch_correction
139 | Filters
140 | Univariate
141 | Multivariate PCA, PLS and OPLS
142
143
144 **Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow**
145
146 .. image:: combinexsannos_workflow_zoom.png
147
148 **General schema of the metabolomic workflow**
149
150 .. image:: combinexsannos_workflow.png
151
152
153 -----------
154 Input files
155 -----------
156
157 +---------------------------+----------------------------+
158 | Parameter : label | Format |
159 +===========================+============================+
160 | Positive RData ion mode | rdata.camera.positive |
161 +---------------------------+----------------------------+
162 | Negative RData ion mode | rdata.camera.negative |
163 +---------------------------+----------------------------+
164
165 ------------
166 Output files
167 ------------
168
169 xset.combinexsAnnos.variableMetadata.tsv
170
171 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
172 | For each metabolite (row) :
173 | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode
174
175 xset.combinexsAnnos.Rdata
176
177 | Rdata file, that be used outside Galaxy in R.
178
179
180 ---------------------------------------------------
181
182 ---------------
183 Working example
184 ---------------
185
186 Input files
187 -----------
188
189 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
190 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**
191
192 Parameters
193 ----------
194
195 | pos -> **positive**
196 | tol -> **2 (default)**
197 | ruleset -> **1,1 (default)**
198
199 Output files
200 ------------
201
202 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
203
204 .. image:: combinexsannos_variableMetadata.png
205
206
207 ---------------------------------------------------
208
209 Changelog/News
210 --------------
211
212 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
213
214 **Version 2.2.5 - 09/04/2019**
215
216 - UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
217
218 - UPGRADE: refactoring of internal code
219
220 **Version 2.2.2 - 01/03/2018**
221
222 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
223
224 **Version 2.0.7 - 29/11/2017**
225
226 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
227
228
229 **Version 2.0.6 - 10/02/2017**
230
231 - IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate)
232
233
234 **Version 2.0.5 - 22/12/2016**
235
236 - IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset)
237
238 **Version 2.0.4 - 21/04/2016**
239
240 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
241
242
243 **Version 2.0.3 - 10/02/2016**
244
245 - BUGFIX: better management of errors. Datasets remained green although the process failed
246
247 - UPDATE: refactoring of internal management of inputs/outputs
248
249
250 **Version 2.0.1 - 07/06/2015**
251
252 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
253
254 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
255
256
257 **Version 2.0.0 - 09/06/2015**
258
259 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
260
261
262 ]]></help>
263
264 <expand macro="citation" />
265
266
267 </tool>