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comparison abims_xcms_group.xml @ 0:f3f97841564f draft

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author lecorguille
date Fri, 07 Aug 2015 11:02:28 -0400
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1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.2">
2
3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</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="2.1">xcms_w4m_script</requirement>
10 </requirements>
11
12 <stdio>
13 <exit_code range="1:" level="fatal" />
14 </stdio>
15
16 <command>
17 xcms.r
18 xfunction group image $image method $methods.method sleep 0.001
19 #if $methods.method == "density":
20 ## minsamp $methods.minsamp
21 minfrac $methods.minfrac
22 bw $methods.bw
23 mzwid $methods.mzwid
24 #if $methods.density_options.option == "show":
25 max $methods.density_options.max
26 #end if
27 #elif $methods.method == "mzClust":
28 mzppm $methods.mzppm
29 mzabs $methods.mzabs
30 minfrac $methods.minfrac
31 ## minsamp $methods.minsamp
32 #else:
33 mzVsRTbalance $methods.mzVsRTbalance
34 mzCheck $methods.mzCheck
35 rtCheck $methods.rtCheck
36 kNN $methods.kNN
37 #end if
38 &amp;&amp; (
39 mv group.RData $xsetRData;
40 mv Rplots.pdf $rplotsPdf
41 );
42 cat xset.log
43 </command>
44
45 <inputs>
46 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
47 <conditional name="methods">
48 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
49 <option value="density" selected="true">density</option>
50 <option value="mzClust" >mzClust</option>
51 <option value="nearest" >nearest</option>
52 </param>
53 <when value="density">
54 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
55 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
56 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
57 <!--
58 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
59 -->
60 <conditional name="density_options">
61 <param name="option" type="select" label="Advanced options">
62 <option value="show">show</option>
63 <option value="hide" selected="true">hide</option>
64 </param>
65 <when value="show">
66 <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
67 </when>
68 <when value="hide">
69 </when>
70 </conditional>
71
72 </when>
73 <when value="mzClust">
74 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
75 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
76 <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" />
77 <!--
78 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
79 -->
80 </when>
81 <when value="nearest">
82 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" />
83 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
84 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
85 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
86 </when>
87 </conditional>
88 <!--
89 <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines">
90 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
91 </param>
92 -->
93
94 </inputs>
95
96 <outputs>
97 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
98 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
99 </outputs>
100
101 <tests>
102 <test>
103 <param name="image" value="xset.RData"/>
104 <param name="methods.method" value="density"/>
105 <param name="methods.bw" value="5"/>
106 <param name="methods.minfrac" value="0.3"/>
107 <param name="methods.mzwid" value="0.01"/>
108 <param name="methods.density_options.option" value="show"/>
109 <param name="methods.density_options.max" value="50"/>
110 <output name="xsetRData" file="xset.group.RData" />
111 <output name="rplotsPdf" file="xset.group.Rplots.pdf" />
112
113 </test>
114 </tests>
115
116 <help>
117
118 .. class:: infomark
119
120 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
121
122 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
123
124 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
125
126
127
128 ---------------------------------------------------
129
130 ==========
131 Xcms.Group
132 ==========
133
134 -----------
135 Description
136 -----------
137
138 After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.
139
140
141
142 -----------------
143 Workflow position
144 -----------------
145
146 **Upstream tools**
147
148 ========================= ================= =================== ==========
149 Name output file format parameter
150 ========================= ================= =================== ==========
151 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
152 ------------------------- ----------------- ------------------- ----------
153 xcms.retcor xset.RData rdata.xcms.retcor RData file
154 ========================= ================= =================== ==========
155
156
157 **Downstream tools**
158
159 +---------------------------+--------------------------------------+
160 | Name | Output file | Format |
161 +===========================+=================+====================+
162 |xcms.retcor | xset.RData | rdata.xcms.group |
163 +---------------------------+--------------------------------------+
164 |xcms.fillPeaks | xset.RData | rdata.xcms.group |
165 +---------------------------+--------------------------------------+
166
167 The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**.
168
169 **General schema of the metabolomic workflow**
170
171 .. image:: xcms_group_workflow.png
172
173
174 -----------
175 Input files
176 -----------
177
178 +---------------------------+-----------------------+
179 | Parameter : num + label | Format |
180 +===========================+=======================+
181 | 1 : RData file | rdata.xcms.group |
182 +---------------------------+-----------------------+
183
184
185 ----------
186 Parameters
187 ----------
188
189 Method to use for grouping
190 --------------------------
191
192 **mzClust**
193
194 | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**.
195
196 **density**
197
198 | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.
199
200 **nearest**
201
202 | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine.
203
204
205 ------------
206 Output files
207 ------------
208
209 xset.group.Rplots.pdf
210
211 xset.group.RData: rdata.xcms.group format
212
213 | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
214
215
216 ------
217
218 .. class:: infomark
219
220 The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.
221
222
223 ---------------------------------------------------
224
225
226 ---------------
227 Working example
228 ---------------
229
230 Input files
231 -----------
232
233 | RData file -> **xset.RData**
234
235 Parameters
236 ----------
237
238 | Method -> **density**
239 | bw -> **5**
240 | minfrac -> **0.3**
241 | mzwid -> **0.01**
242 | Advanced options: **show**
243 | max -> **50**
244
245
246 Output files
247 ------------
248
249 | **1) xset.RData: RData file**
250
251 | **2) Example of an xset.group.Rplots pdf file**
252
253 .. image:: xcms_group.png
254 :width: 700
255
256
257 </help>
258
259
260 <citations>
261 <citation type="doi">10.1021/ac051437y</citation>
262 <citation type="doi">10.1093/bioinformatics/btu813</citation>
263 </citations>
264
265
266 </tool>