Mercurial > repos > lecorguille > xcms_group
annotate abims_xcms_group.xml @ 4:2db1d1d0f131 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author | lecorguille |
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date | Fri, 08 Apr 2016 10:39:09 -0400 |
parents | 98e33cdf0eb1 |
children | 0306a96cc446 |
rev | line source |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.5"> |
0 | 2 |
3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description> | |
4 | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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5 <macros> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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6 <import>macros.xml</import> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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7 </macros> |
0 | 8 |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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9 <expand macro="requirements"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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10 <expand macro="stdio"/> |
0 | 11 |
3 | 12 <command><![CDATA[ |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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13 @COMMAND_XCMS_SCRIPT@ |
3 | 14 xfunction group |
15 image $image | |
16 | |
17 xsetRdataOutput $xsetRData | |
18 rplotspdf $rplotsPdf | |
19 | |
20 method $methods.method sleep 0.001 | |
0 | 21 #if $methods.method == "density": |
22 ## minsamp $methods.minsamp | |
23 minfrac $methods.minfrac | |
24 bw $methods.bw | |
25 mzwid $methods.mzwid | |
26 #if $methods.density_options.option == "show": | |
27 max $methods.density_options.max | |
28 #end if | |
29 #elif $methods.method == "mzClust": | |
30 mzppm $methods.mzppm | |
31 mzabs $methods.mzabs | |
32 minfrac $methods.minfrac | |
33 ## minsamp $methods.minsamp | |
34 #else: | |
35 mzVsRTbalance $methods.mzVsRTbalance | |
36 mzCheck $methods.mzCheck | |
37 rtCheck $methods.rtCheck | |
38 kNN $methods.kNN | |
39 #end if | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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40 @COMMAND_LOG_EXIT@ |
3 | 41 ]]></command> |
0 | 42 |
43 <inputs> | |
44 <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.)" /> | |
45 <conditional name="methods"> | |
46 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> | |
47 <option value="density" selected="true">density</option> | |
48 <option value="mzClust" >mzClust</option> | |
49 <option value="nearest" >nearest</option> | |
50 </param> | |
51 <when value="density"> | |
52 <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" /> | |
53 <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" /> | |
54 <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 " /> | |
55 <!-- | |
56 <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 " /> | |
57 --> | |
58 <conditional name="density_options"> | |
59 <param name="option" type="select" label="Advanced options"> | |
60 <option value="show">show</option> | |
61 <option value="hide" selected="true">hide</option> | |
62 </param> | |
63 <when value="show"> | |
64 <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" /> | |
65 </when> | |
66 <when value="hide"> | |
67 </when> | |
68 </conditional> | |
69 | |
70 </when> | |
71 <when value="mzClust"> | |
72 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" /> | |
73 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" /> | |
74 <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" /> | |
75 <!-- | |
76 <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 " /> | |
77 --> | |
78 </when> | |
79 <when value="nearest"> | |
80 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" /> | |
81 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" /> | |
82 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" /> | |
83 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" /> | |
84 </when> | |
85 </conditional> | |
86 <!-- | |
87 <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"> | |
88 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/> | |
89 </param> | |
90 --> | |
91 | |
92 </inputs> | |
93 | |
94 <outputs> | |
95 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/> | |
96 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> | |
3 | 97 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
0 | 98 </outputs> |
99 | |
100 <tests> | |
101 <test> | |
102 <param name="image" value="xset.RData"/> | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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changeset
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103 <param name="methods|method" value="density"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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changeset
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104 <param name="methods|bw" value="5"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
3
diff
changeset
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105 <param name="methods|minfrac" value="0.3"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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changeset
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106 <param name="methods|mzwid" value="0.01"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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changeset
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107 <param name="methods|density_options|option" value="show"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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changeset
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108 <param name="methods|density_options|max" value="50"/> |
3 | 109 <output name="log"> |
110 <assert_contents> | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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111 <has_text text="object with 4 samples" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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112 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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113 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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114 <has_text text="Peaks: 59359 (about 14840 per sample)" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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115 <has_text text="Peak Groups: 48998" /> |
3 | 116 <has_text text="Sample classes: bio, blank" /> |
117 </assert_contents> | |
118 </output> | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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119 </test> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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120 <test> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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121 <param name="image" value="xset.group.retcor.RData"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
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122 <param name="methods|method" value="density"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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123 <param name="methods|bw" value="5"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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124 <param name="methods|minfrac" value="0.3"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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125 <param name="methods|mzwid" value="0.01"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
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126 <param name="methods|density_options|option" value="show"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
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127 <param name="methods|density_options|max" value="50"/> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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128 <output name="log"> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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129 <assert_contents> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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130 <has_text text="object with 4 samples" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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131 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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132 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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changeset
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133 <has_text text="Peaks: 59359 (about 14840 per sample)" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
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134 <has_text text="Peak Groups: 48958" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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135 <has_text text="Sample classes: bio, blank" /> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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136 </assert_contents> |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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137 </output> |
0 | 138 </test> |
139 </tests> | |
140 | |
3 | 141 <help><![CDATA[ |
0 | 142 |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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143 @HELP_AUTHORS@ |
0 | 144 |
145 ========== | |
146 Xcms.Group | |
147 ========== | |
148 | |
149 ----------- | |
150 Description | |
151 ----------- | |
152 | |
153 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. | |
154 | |
155 | |
156 | |
157 ----------------- | |
158 Workflow position | |
159 ----------------- | |
160 | |
161 **Upstream tools** | |
162 | |
163 ========================= ================= =================== ========== | |
164 Name output file format parameter | |
165 ========================= ================= =================== ========== | |
166 xcms.xcmsSet xset.RData rdata.xcms.raw RData file | |
167 ------------------------- ----------------- ------------------- ---------- | |
168 xcms.retcor xset.RData rdata.xcms.retcor RData file | |
169 ========================= ================= =================== ========== | |
170 | |
171 | |
172 **Downstream tools** | |
173 | |
174 +---------------------------+--------------------------------------+ | |
175 | Name | Output file | Format | | |
176 +===========================+=================+====================+ | |
177 |xcms.retcor | xset.RData | rdata.xcms.group | | |
178 +---------------------------+--------------------------------------+ | |
179 |xcms.fillPeaks | xset.RData | rdata.xcms.group | | |
180 +---------------------------+--------------------------------------+ | |
181 | |
182 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**. | |
183 | |
184 **General schema of the metabolomic workflow** | |
185 | |
186 .. image:: xcms_group_workflow.png | |
187 | |
188 | |
189 ----------- | |
190 Input files | |
191 ----------- | |
192 | |
193 +---------------------------+-----------------------+ | |
194 | Parameter : num + label | Format | | |
195 +===========================+=======================+ | |
196 | 1 : RData file | rdata.xcms.group | | |
197 +---------------------------+-----------------------+ | |
198 | |
199 | |
200 ---------- | |
201 Parameters | |
202 ---------- | |
203 | |
204 Method to use for grouping | |
205 -------------------------- | |
206 | |
207 **mzClust** | |
208 | |
209 | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**. | |
210 | |
211 **density** | |
212 | |
213 | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. | |
214 | |
215 **nearest** | |
216 | |
217 | 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. | |
218 | |
219 | |
220 ------------ | |
221 Output files | |
222 ------------ | |
223 | |
224 xset.group.Rplots.pdf | |
225 | |
226 xset.group.RData: rdata.xcms.group format | |
227 | |
228 | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks). | |
229 | |
230 | |
231 ------ | |
232 | |
233 .. class:: infomark | |
234 | |
235 The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool. | |
236 | |
237 | |
238 --------------------------------------------------- | |
239 | |
240 | |
241 --------------- | |
242 Working example | |
243 --------------- | |
244 | |
245 Input files | |
246 ----------- | |
247 | |
248 | RData file -> **xset.RData** | |
249 | |
250 Parameters | |
251 ---------- | |
252 | |
253 | Method -> **density** | |
254 | bw -> **5** | |
255 | minfrac -> **0.3** | |
256 | mzwid -> **0.01** | |
257 | Advanced options: **show** | |
258 | max -> **50** | |
259 | |
260 | |
261 Output files | |
262 ------------ | |
263 | |
264 | **1) xset.RData: RData file** | |
265 | |
266 | **2) Example of an xset.group.Rplots pdf file** | |
267 | |
268 .. image:: xcms_group.png | |
269 :width: 700 | |
270 | |
271 | |
3 | 272 --------------------------------------------------- |
2 | 273 |
3 | 274 Changelog/News |
275 -------------- | |
276 | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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277 **Version 2.0.5 - 04/04/2016** |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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278 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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279 - TEST: refactoring to pass planemo test using conda dependencies |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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280 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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281 |
3 | 282 **Version 2.0.4 - 10/02/2016** |
283 | |
284 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
285 | |
286 - UPDATE: refactoring of internal management of inputs/outputs | |
287 | |
288 - UPDATE: refactoring to feed the new report tool | |
289 | |
290 | |
291 **Version 2.0.2 - 02/06/2015** | |
292 | |
293 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. | |
294 | |
295 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
296 | |
297 | |
298 ]]></help> | |
0 | 299 |
300 | |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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301 <expand macro="citation" /> |
0 | 302 |
303 | |
304 </tool> |