Mercurial > repos > lecorguille > xcms_fillpeaks
comparison abims_xcms_fillPeaks.xml @ 9:ee29f0a6e361 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author | lecorguille |
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date | Mon, 30 Jan 2017 08:53:48 -0500 |
parents | cce30b3398e0 |
children | de0d85537ee3 |
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8:cce30b3398e0 | 9:ee29f0a6e361 |
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1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.7"> | 1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8"> |
2 | 2 |
3 <description>Integrate the signal in the region of that peak group not represented and create a new peak</description> | 3 <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description> |
4 | 4 |
5 <macros> | 5 <macros> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
7 </macros> | 7 </macros> |
8 | 8 |
9 <expand macro="requirements"/> | 9 <expand macro="requirements"/> |
10 <expand macro="stdio"/> | 10 <expand macro="stdio"/> |
11 | 11 |
12 <command><![CDATA[ | 12 <command><![CDATA[ |
13 @COMMAND_XCMS_SCRIPT@ | 13 @COMMAND_XCMS_SCRIPT@ |
14 xfunction fillPeaks | 14 xfunction fillPeaks |
15 image $image | 15 image $image |
16 | 16 |
17 xsetRdataOutput $xsetRData | 17 xsetRdataOutput $xsetRData |
18 | 18 |
19 method $method | 19 method $method |
20 | 20 |
21 #if $peaklist.peaklistBool | |
22 variableMetadataOutput $variableMetadata | |
23 dataMatrixOutput $dataMatrix | |
24 convertRTMinute $peaklist.convertRTMinute | |
25 numDigitsMZ $peaklist.numDigitsMZ | |
26 numDigitsRT $peaklist.numDigitsRT | |
27 intval $peaklist.intval | |
28 #end if | |
29 | |
21 @COMMAND_ZIPFILE_LOAD@ | 30 @COMMAND_ZIPFILE_LOAD@ |
22 | 31 |
23 @COMMAND_LOG_EXIT@ | 32 @COMMAND_LOG_EXIT@ |
24 | 33 |
25 ]]></command> | 34 ]]></command> |
26 | 35 |
27 <inputs> | 36 <inputs> |
28 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> | 37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" /> |
29 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> | 38 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> |
30 <option value="chrom" selected="true">chrom</option> | 39 <option value="chrom" selected="true">chrom</option> |
31 <option value="MSW" >MSW</option> | 40 <option value="MSW" >MSW</option> |
32 </param> | 41 </param> |
33 | 42 <conditional name="peaklist"> |
43 <param name="peaklistBool" type="boolean" label="Get a Peak List" /> | |
44 <when value="true"> | |
45 <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"/> | |
46 <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" /> | |
47 <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" /> | |
48 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> | |
49 <option value="into" selected="true">into</option> | |
50 <option value="maxo">maxo</option> | |
51 <option value="intb">intb</option> | |
52 </param> | |
53 </when> | |
54 <when value="false" /> | |
55 </conditional> | |
34 <expand macro="zipfile_load"/> | 56 <expand macro="zipfile_load"/> |
35 | 57 |
36 </inputs> | 58 </inputs> |
37 | 59 |
38 <outputs> | 60 <outputs> |
39 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> | 61 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> |
62 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv"> | |
63 <filter>(peaklist['peaklistBool'])</filter> | |
64 </data> | |
65 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" > | |
66 <filter>(peaklist['peaklistBool'])</filter> | |
67 </data> | |
40 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> | 68 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
41 </outputs> | 69 </outputs> |
42 | 70 |
43 <tests> | 71 <tests> |
44 <!--<test> | 72 <!--<test> |
45 <param name="image" value="xset.group.retcor.group.RData"/> | 73 <param name="image" value="xset.group.retcor.group.RData"/> |
46 <param name="method" value="chrom"/> | 74 <param name="method" value="chrom"/> |
47 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> | 75 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> |
57 </output> | 85 </output> |
58 </test>--> | 86 </test>--> |
59 <test> | 87 <test> |
60 <param name="image" value="faahKO.xset.group.retcor.group.RData"/> | 88 <param name="image" value="faahKO.xset.group.retcor.group.RData"/> |
61 <param name="method" value="chrom"/> | 89 <param name="method" value="chrom"/> |
90 <conditional name="peaklist"> | |
91 <param name="convertRTMinute" value="false" /> | |
92 <param name="peaklistBool" value="true" /> | |
93 <param name="numDigitsMZ" value="4" /> | |
94 <param name="numDigitsRT" value="1" /> | |
95 </conditional> | |
62 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> | 96 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> |
63 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> | 97 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> |
64 <output name="log"> | 98 <output name="log"> |
65 <assert_contents> | 99 <assert_contents> |
66 <has_text text="object with 4 samples" /> | 100 <has_text text="object with 4 samples" /> |
69 <has_text text="Peaks: 32720 (about 8180 per sample)" /> | 103 <has_text text="Peaks: 32720 (about 8180 per sample)" /> |
70 <has_text text="Peak Groups: 8157" /> | 104 <has_text text="Peak Groups: 8157" /> |
71 <has_text text="Sample classes: KO, WT" /> | 105 <has_text text="Sample classes: KO, WT" /> |
72 </assert_contents> | 106 </assert_contents> |
73 </output> | 107 </output> |
108 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" /> | |
109 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" /> | |
74 </test> | 110 </test> |
75 </tests> | 111 </tests> |
76 | 112 |
77 <help><![CDATA[ | 113 <help><![CDATA[ |
78 | 114 |
79 @HELP_AUTHORS@ | 115 @HELP_AUTHORS@ |
80 | 116 |
81 ============== | 117 ============== |
82 Xcms.fillPeaks | 118 Xcms.fillPeaks |
83 ============== | 119 ============== |
84 | 120 |
85 ----------- | 121 ----------- |
86 Description | 122 Description |
87 ----------- | 123 ----------- |
88 | 124 |
125 **Integrate areas of missing peaks** | |
89 For each sample, identify peak groups where that sample is not | 126 For each sample, identify peak groups where that sample is not |
90 represented. For each of those peak groups, integrate the signal | 127 represented. For each of those peak groups, integrate the signal |
91 in the region of that peak group and create a new peak. | 128 in the region of that peak group and create a new peak. |
92 | 129 |
93 According to the type of raw-data there are 2 | 130 According to the type of raw-data there are 2 |
115 **Downstream tools** | 152 **Downstream tools** |
116 | 153 |
117 +---------------------------+------------------+-----------------------+ | 154 +---------------------------+------------------+-----------------------+ |
118 | Name | Output file | Format | | 155 | Name | Output file | Format | |
119 +===========================+==================+=======================+ | 156 +===========================+==================+=======================+ |
120 |xcms.diffreport | xset.retcor.RData| rdata.xcms.fillpeaks | | 157 |CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks | |
121 +---------------------------+------------------+-----------------------+ | 158 +---------------------------+------------------+-----------------------+ |
122 |xcms.annotateDiffreport | xset.retcor.RData| rdata.xcms.fillpeaks | | 159 |xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks | |
123 +---------------------------+------------------+-----------------------+ | 160 +---------------------------+------------------+-----------------------+ |
124 | 161 |
125 The output file **xset.fillpeaks** is an RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool as an next step of the workflow. | 162 The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow. |
126 | 163 |
127 | 164 |
128 **General schema of the metabolomic workflow** | 165 **General schema of the metabolomic workflow** |
129 | 166 |
130 .. image:: xcms_fillpeaks_workflow.png | 167 .. image:: xcms_fillpeaks_workflow.png |
157 | 194 |
158 **MSW** | 195 **MSW** |
159 | 196 |
160 | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra. | 197 | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra. |
161 | 198 |
199 | |
200 Get a Peak List | |
201 --------------- | |
202 | |
203 If 'true', the module generates two additional files corresponding to the peak list: | |
204 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time) | |
205 - the data matrix (corresponding to related intensities) | |
206 | |
207 **decimal places for [mass or retention time] values in identifiers** | |
208 | |
209 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. | |
210 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. | |
211 | Theses parameters do not affect decimal places in columns other than the identifier one. | |
212 | |
213 **Reported intensity values** | |
214 | |
215 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: | |
216 | - into: integrated area of original (raw) peak | |
217 | - maxo: maximum intensity of original (raw) peak | |
218 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) | |
219 | |
162 ------------ | 220 ------------ |
163 Output files | 221 Output files |
164 ------------ | 222 ------------ |
165 | 223 |
166 xset.fillPeaks.RData : rdata.xcms.fillpeaks format | 224 xset.fillPeaks.RData : rdata.xcms.fillpeaks format |
167 | 225 |
168 | Rdata file that will be used in the **xcms.diffreport** or **xcms.annotateDiffreport** step of the workflow. | 226 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow. |
169 | 227 |
228 xset.variableMetadata.tsv : tabular format | |
229 | |
230 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter* modules. | |
231 | |
232 xset.dataMatrix.tsv : tabular format | |
233 | |
234 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter* modules. | |
235 | |
170 ------ | 236 ------ |
171 | 237 |
172 .. class:: infomark | 238 .. class:: infomark |
173 | 239 |
174 The output file is an group.RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool. | 240 The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool. |
175 | 241 |
176 | 242 |
177 --------------------------------------------------- | 243 --------------------------------------------------- |
178 | 244 |
179 --------------- | 245 --------------- |
180 Working example | 246 Working example |
181 --------------- | 247 --------------- |
187 | 253 |
188 Parameters | 254 Parameters |
189 ---------- | 255 ---------- |
190 | 256 |
191 | method -> **chrom** | 257 | method -> **chrom** |
192 | 258 | Get a Peak List -> **false** |
259 | |
193 | 260 |
194 Output files | 261 Output files |
195 ------------ | 262 ------------ |
196 | 263 |
197 | **xset.fillPeaks.RData: RData file** | 264 | **xset.fillPeaks.RData: RData file** |
200 --------------------------------------------------- | 267 --------------------------------------------------- |
201 | 268 |
202 Changelog/News | 269 Changelog/News |
203 -------------- | 270 -------------- |
204 | 271 |
272 **Version 2.0.8 - 22/12/2016** | |
273 | |
274 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate | |
275 | |
205 **Version 2.0.7 - 06/07/2016** | 276 **Version 2.0.7 - 06/07/2016** |
206 | 277 |
207 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 | 278 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 |
208 | 279 |
209 **Version 2.0.6 - 04/04/2016** | 280 **Version 2.0.6 - 04/04/2016** |