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comparison abims_CAMERA_combinexsAnnos.xml @ 0:0c730c636867 draft

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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.1">
2
3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
4
5 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="binary">Rscript</requirement>
8 <requirement type="package" version="1.44.0">xcms</requirement>
9 <requirement type="package" version="1.22.0">camera</requirement>
10 <requirement type="package" version="2.1">camera_w4m_script</requirement>
11 </requirements>
12
13 <stdio>
14 <exit_code range="1:" level="fatal" />
15 </stdio>
16
17 <command>
18 CAMERA.r
19 xfunction combinexsAnnos image_pos $image_pos image_neg $image_neg
20 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta &amp;&amp; (
21 mv variableMetadata.tsv $variableMetadata);
22 cat xset.log
23 </command>
24
25 <inputs>
26 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
27 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
28
29 <param name="pos" type="select" label="Returned peaklist polarity mode">
30 <option value="TRUE" selected="true">positive</option>
31 <option value="FALSE" >negative</option>
32 </param>
33
34 <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
35 <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
36 <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>
37 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
38
39 </inputs>
40
41 <outputs>
42 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />
43 <!--
44 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" />
45 -->
46 </outputs>
47
48 <tests>
49 <test>
50 <!-- TODO: generer des vrais dataset pos et neg-->
51 <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
52 <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
53 <param name="pos" value="TRUE"/>
54 <param name="tol" value="2"/>
55 <param name="ruleset" value="1,1"/>
56 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
57 </test>
58 </tests>
59
60
61 <help>
62
63 .. class:: infomark
64
65 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
66
67 .. class:: infomark
68
69 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
70
71 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
72
73 ---------------------------------------------------
74
75
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 **General schema of the metabolomic workflow**
145
146 .. image:: combinexsannos_workflow.png
147
148
149 -----------
150 Input files
151 -----------
152
153 +---------------------------+----------------------------+
154 | Parameter : label | Format |
155 +===========================+============================+
156 | Positive RData ion mode | rdata.camera.positive |
157 +---------------------------+----------------------------+
158 | Negative RData ion mode | rdata.camera.negative |
159 +---------------------------+----------------------------+
160
161 ------------
162 Output files
163 ------------
164
165 xset.combinexsAnnos.variableMetadata.tsv
166
167 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
168 | For each metabolite (row) :
169 | 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
170
171 xset.combinexsAnnos.Rdata
172
173 | Rdata file, that be used outside Galaxy in R.
174
175
176 ---------------------------------------------------
177
178 ---------------
179 Working example
180 ---------------
181
182 Input files
183 -----------
184
185 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
186 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**
187
188 Parameters
189 ----------
190
191 | pos -> **positive**
192 | tol -> **2 (default)**
193 | ruleset -> **1,1 (default)**
194
195 Output files
196 ------------
197
198 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
199
200 .. image:: combinexsannos_variableMetadata.png
201
202 </help>
203
204 <citations>
205 <citation type="doi"> 10.1021/ac202450g</citation>
206 <citation type="doi">10.1093/bioinformatics/btu813</citation>
207 </citations>
208
209
210 </tool>
211
212