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comparison ProbMetab.xml @ 3:abcfa1648b66 draft

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planemo upload commit c897279aa8cae0a4ad889bb05b143f32d2b6d712
author lecorguille
date Fri, 07 Apr 2017 07:14:12 -0400
parents c4bd0c40eb3b
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2:3a9914b37f2f 3:abcfa1648b66
1 <tool id="Probmetab" name="ProbMetab Tool" version="1.0.1"> 1 <tool id="Probmetab" name="ProbMetab Tool" version="1.1.0">
2 2
3 <description>Wrapper function for ProbMetab R package.</description> 3 <description>Wrapper function for ProbMetab R package.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <command> 12 <command>
13 @COMMAND_CAMERA_SCRIPT@ 13 @COMMAND_CAMERA_SCRIPT@
14 #if $acquisition_options.mode == "one": 14 #if $acquisition_options.mode == "one":
15 mode_acquisition $acquisition_options.mode xa $acquisition_options.xa 15 mode_acquisition $acquisition_options.mode
16 image '$acquisition_options.image'
16 ##if $acquisition_options.xsetnofill_options.option == "show": 17 ##if $acquisition_options.xsetnofill_options.option == "show":
17 ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill 18 ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill
18 ##end if 19 ##end if
20
21 @COMMAND_FILE_LOAD_ONE@
22
19 #else 23 #else
20 mode_acquisition $acquisition_options.mode inputs_mode $acquisition_options.input_mode.option 24 mode_acquisition $acquisition_options.mode
25 inputs_mode $acquisition_options.input_mode.option
21 #if $acquisition_options.input_mode.option== "two": 26 #if $acquisition_options.input_mode.option== "two":
22 27
23 image_pos $acquisition_options.input_mode.image_pos image_neg $acquisition_options.input_mode.image_neg 28 image_pos '$acquisition_options.input_mode.image_pos'
24 ##if $acquisition_options.input_mode.xsetnofill_options.option == "show": 29 image_neg '$acquisition_options.input_mode.image_neg'
25 ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill 30 ##if $acquisition_options.input_mode.xsetnofill_options.option == "show":
26 ##end if 31 ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill
32 ##xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill
33 ##end if
34
35 @COMMAND_FILE_LOAD_POSITIVE@
36 @COMMAND_FILE_LOAD_NEGATIVE@
27 ##else 37 ##else
28 ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos image_pos $acquisition_options.input_mode.image_pos 38 ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos
39 ##image_pos $acquisition_options.input_mode.image_pos
29 #end if 40 #end if
30 41
31 #end if 42 #end if
32 43
33 #if $option_toexclude.option == "show": 44 ## Extraction of CAMERA annotation [get.annot]
34 toexclude $option_toexclude.toexclude 45 allowMiss $getannot.allowMiss
46 #if $getannot.option_toexclude.option == "show":
47 toexclude $getannot.option_toexclude.toexclude
35 #end if 48 #end if
36 allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol 49
37 opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob 50 ## Database matching [create.reactionM]
38 51 kegg_db $db.kegg_db
39 @COMMAND_ZIPFILE_LOAD@ 52 ppm_tol $db.ppm_tol
53
54 ## Probability calculations matrix export [export.class.table]
55 prob $export.prob
56 html $export.html
57
58 ## Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]
59 opt $reac2cor.opt
60 corprob $reac2cor.corprob
61 pcorprob $reac2cor.pcorprob
62 corths $reac2cor.corths
63
64 @COMMAND_LOG_EXIT@
40 65
41 </command> 66 </command>
42 67
43 <inputs> 68 <inputs>
44 69
45 <conditional name="acquisition_options"> 70 <conditional name="acquisition_options">
46 <param name="mode" type="select" label="Choose your acquisition mode" > 71 <param name="mode" type="select" label="Choose your acquisition mode" >
47 <option value="one" selected="true" >One acquisition charge mode</option> 72 <option value="one" selected="true" >One acquisition charge mode</option>
48 <option value="two" >Two acquisition charge mode (positif and negatif)</option> 73 <option value="two" >Two acquisition charge mode (positif and negatif)</option>
49 </param> 74 </param>
50 75
51 <!-- One acquisition mode--> 76 <!-- One acquisition mode-->
52 <when value="one"> 77 <when value="one">
53 <param name="xa" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " /> 78 <param name="image" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " />
54 <!-- 79 <!--
55 <conditional name="xsetnofill_options"> 80 <conditional name="xsetnofill_options">
56 <param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." > 81 <param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." >
57 <option value="show">show</option> 82 <option value="show">show</option>
58 <option value="hide" selected="true">hide</option> 83 <option value="hide" selected="true">hide</option>
59 </param> 84 </param>
60 <when value="show"> 85 <when value="show">
61 <param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" /> 86 <param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" />
62 </when> 87 </when>
63 88 </conditional>
64 </conditional> 89 -->
65 --> 90 <expand macro="input_file_load"/>
66 </when> 91 </when>
67 <!-- Two acquisition modes--> 92 <!-- Two acquisition modes-->
68 <when value="two"> 93 <when value="two">
69 94 <conditional name="input_mode">
70 95 <param name="option" type="select" label="Choose your input type method:" >
71 <conditional name="input_mode"> 96 <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> -->
72 <param name="option" type="select" label="Choose your input type method:" > 97 <option value="two" selected="true">Rdata inputs from annotate</option>
73 <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> --> 98 </param>
74 <option value="two" selected="true">Rdata inputs from annotate</option> 99 <!--
75 </param> 100 <when value="one">
76 <!-- 101 <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " />
77 <when value="one"> 102 <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " />
78 <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " /> 103 </when>
79 <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " /> 104 -->
80 </when> 105 <when value="two">
81 --> 106 <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " />
82 <when value="two"> 107 <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" />
83 <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " /> 108 <!--
84 <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" /> 109 <conditional name="xsetnofill_options">
85 <!-- 110 <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." >
86 <conditional name="xsetnofill_options"> 111 <option value="show">show</option>
87 <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." > 112 <option value="hide" selected="true">hide</option>
88 <option value="show">show</option> 113 </param>
89 <option value="hide" selected="true">hide</option> 114 <when value="show">
90 </param> 115 <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" />
91 <when value="show"> 116 <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" />
92 <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" /> 117 </when>
93 <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" /> 118 </conditional>
94 </when> 119 -->
95 </conditional> 120 </when>
96 --> 121 </conditional>
97 </when> 122 <expand macro="input_file_load" polarity="Positive"/>
98 </conditional> 123 <expand macro="input_file_load" polarity="Negative"/>
99 </when> 124 </when>
100
101 </conditional> 125 </conditional>
102 126
103 127 <section name="getannot" title="Extraction of CAMERA annotation [get.annot]" expanded="True">
104 <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." /> 128 <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." />
105 <conditional name="option_toexclude"> 129 <conditional name="option_toexclude">
106 <param name="option" type="select" label="Exclude samples" > 130 <param name="option" type="select" label="Exclude samples" >
107 <option value="show">show</option> 131 <option value="show">show</option>
108 <option value="hide" selected="true">hide</option> 132 <option value="hide" selected="true">hide</option>
109 </param> 133 </param>
110 <when value="show"> 134 <when value="show">
111 <param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" /> 135 <param name="toexclude" type="text" value="blank,medium,QC" label="Samples to be excluded of peak counting to non-annotated peak selection." help="[toexclude]" />
112 </when> 136 </when>
113 <when value="hide" /> 137 <when value="hide" />
114 </conditional> 138 </conditional>
139 </section>
140
141 <section name="db" title="Database matching [create.reactionM]" expanded="True">
142 <param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" >
143 <validator type="empty_field"/>
144 </param>
145 <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol]" />
146 <!--
147 <conditional name="useIso_options">
148 <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" >
149 <option value="show">Yes</option>
150 <option value="hide" selected="true">No</option>
151 </param>
152 <when value="show">
153 <param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." >
154 <option value="1">1</option>
155 <option value="2" selected="true">2</option>
156 </param>
157 </when>
158 </conditional>
159 -->
160 </section>
161
162 <section name="export" title="Probability calculations matrix export [export.class.table]" expanded="True">
163 <param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] Default is 'count'. See the tool help for more details." >
164 <option value="count" selected="true">Count</option>
165 <option value="mean">Mean</option>
166 </param>
167
168 <param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help="[html] This parameter uses the raw data to plot EICs and may be time consuming." />
169 </section>
170
171 <section name="reac2cor" title="Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]" expanded="True">
172 <param name="opt" type="select" label="Correlation option" help="[opt] cor for correlation, and pcor for partial correlation." >
173 <option value="cor" selected="true">cor</option>
174 <option value="pcor">pcor</option>
175 </param>
176
177 <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob]" />
178
179 <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob]" />
180 <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths]" />
181 </section>
182
115 <!-- 183 <!--
116 <conditional name="useIso_options"> 184 <section name="cytoscape" title="CytoScape options">
117 <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" > 185 <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
118 <option value="show">Yes</option> 186 " />
119 <option value="hide" selected="true">No</option> 187 </section>
120 </param>
121 <when value="show">
122 <param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." >
123 <option value="1">1</option>
124 <option value="2" selected="true">2</option>
125 </param>
126 </when>
127 </conditional>
128 --> 188 -->
129 <param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help=" [html] (export.class.table function).This parameter uses the raw data to plot EICs and may be time consuming." /> 189
130
131 <param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" >
132 <validator type="empty_field"/>
133 </param>
134 <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol] (create.reactionMfunction) " />
135
136
137 <param name="opt" type="select" label="Correlation option" help="[opt] (reac2cor function) cor for correlation, and pcor for partial correlation." >
138 <option value="cor" selected="true">cor</option>
139 <option value="pcor">pcor</option>
140 </param>
141
142
143 <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " />
144
145
146 <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob](reac2cor function)" />
147 <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths] (reac2cor function)" />
148
149 <param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] (export.class.table function). Default is 'count'. See the tool help for more details." >
150 <option value="count" selected="true">Count</option>
151 <option value="mean">Mean</option>
152 </param>
153 <!--
154 <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
155 " />
156
157 -->
158
159 <expand macro="zipfile_load"/>
160 </inputs> 190 </inputs>
161 191
162 <outputs> 192 <outputs>
163 <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> --> 193 <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> -->
164 <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" > 194 <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" >
165 <filter>(html)</filter> 195 <filter>(export['html'])</filter>
166 </data> 196 </data>
167 <data name="tsv_output" format="tabular" from_work_dir="Analysis_Report.tsv" label="Probmetab.CytoScape_output_Attribute_List.tsv" /> 197 <data name="tsv_output" format="tabular" from_work_dir="Analysis_Report.tsv" label="Probmetab.CytoScape_output_Attribute_List.tsv" />
168 <data name="eics" format="zip" from_work_dir="Analysis_Report.zip" label="Probmetab.Analysis_Report_EICs_plots.zip" > 198 <data name="eics" format="zip" from_work_dir="Analysis_Report.zip" label="Probmetab.Analysis_Report_EICs_plots.zip" >
169 <filter>(html)</filter> 199 <filter>(export['html'])</filter>
170 </data> 200 </data>
171 <data name="sif_output" format="tabular" from_work_dir="sif.tsv" label="Probmetab.CytoScape_output.sif" /> 201 <data name="sif_output" format="tabular" from_work_dir="sif.tsv" label="Probmetab.CytoScape_output.sif" />
172 <data name="log" format="txt" from_work_dir="probmetab.log" label="Probmetab.log" />
173 <data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" > 202 <data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" >
174 <filter>(acquisition_options['mode'] == 'one')</filter> 203 <filter>(acquisition_options['mode'] == 'one')</filter>
175 </data> 204 </data>
176 205
177 <data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" > 206 <data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" >
178 <filter>(acquisition_options['mode'] == 'two')</filter> 207 <filter>(acquisition_options['mode'] == 'two')</filter>
179 </data> 208 </data>
180 <data name="variableMetadata_Positive" format="tabular" from_work_dir="variableMetadata_Positive.tsv" label="variableMetadata_Positive.tsv" > 209 <data name="variableMetadata_Positive" format="tabular" from_work_dir="variableMetadata_Positive.tsv" label="variableMetadata_Positive.tsv" >
181 <filter>(acquisition_options['mode'] == 'two')</filter> 210 <filter>(acquisition_options['mode'] == 'two')</filter>
182 </data> 211 </data>
183 <data name="variableMetadata_Negative" format="tabular" from_work_dir="variableMetadata_Negative.tsv" label="variableMetadata_Negative.tsv" > 212 <data name="variableMetadata_Negative" format="tabular" from_work_dir="variableMetadata_Negative.tsv" label="variableMetadata_Negative.tsv" >
184 <filter>(acquisition_options['mode'] == 'two')</filter> 213 <filter>(acquisition_options['mode'] == 'two')</filter>
185 </data> 214 </data>
186 215
187 </outputs> 216 </outputs>
188 217
189 <tests> 218 <tests>
190 <test> 219 <test>
191 <param name="acquisition_options|mode" value="one" /> 220 <conditional name="acquisition_options">
192 <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> 221 <param name="mode" value="one" />
193 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> 222 <param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
194 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> 223 </conditional>
195 <output name="log"> 224 <expand macro="test_commun"/>
196 <assert_contents> 225 <expand macro="test_file_load_zip"/>
197 <has_text text="ko15 ko16 wt15 wt16" /> 226 <assert_stdout>
198 <has_text text="Step 1... determine cutoff point" /> 227 <has_text text="Step 1... determine cutoff point" />
199 <has_text text="Step 2... estimate parameters of null distribution and eta0" /> 228 <has_text text="Step 2... estimate parameters of null distribution and eta0" />
200 <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" /> 229 <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" />
201 <has_text text="Step 4... compute q-values and local fdr" /> 230 <has_text text="Step 4... compute q-values and local fdr" />
202 </assert_contents> 231 </assert_stdout>
203 </output> 232 </test>
233 <test>
234 <conditional name="acquisition_options">
235 <param name="mode" value="one" />
236 <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
237 </conditional>
238 <expand macro="test_commun"/>
239 <expand macro="test_file_load_single"/>
240 <assert_stdout>
241 <has_text text="Step 1... determine cutoff point" />
242 <has_text text="Step 2... estimate parameters of null distribution and eta0" />
243 <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" />
244 <has_text text="Step 4... compute q-values and local fdr" />
245 </assert_stdout>
204 </test> 246 </test>
205 </tests> 247 </tests>
206 248
207 249
208 <help> 250 <help>
209 251
210 @HELP_AUTHORS@ 252 @HELP_AUTHORS@
211 253
212 ========= 254 =========
213 ProbMetab 255 ProbMetab
214 ========= 256 =========
223 265
224 266
225 **Details** 267 **Details**
226 268
227 ProbMetab assumes peak detection, retention time correction and peak grouping [4, 5] in order to 269 ProbMetab assumes peak detection, retention time correction and peak grouping [4, 5] in order to
228 perform mass peak to compound assignment. 270 perform mass peak to compound assignment.
229 271
230 Once the initial annotation for different forms of the same ion (adducts and isotopes), is defined, 272 Once the initial annotation for different forms of the same ion (adducts and isotopes), is defined,
231 one can seek for a non-redundant set of putative molecules (after charge and possible adduct 273 one can seek for a non-redundant set of putative molecules (after charge and possible adduct
232 correction) for further inference of compound identity. 274 correction) for further inference of compound identity.
233 275
234 Experience shows that standard mass rules for adduct search may lose peaks, and specific rule tables must be setup for a given 276 Experience shows that standard mass rules for adduct search may lose peaks, and specific rule tables must be setup for a given
235 experimental condition. In order to address this issue, a flexible workflow, which allows users to 277 experimental condition. In order to address this issue, a flexible workflow, which allows users to
236 integrate different methods, would improve true molecular ions recovery. 278 integrate different methods, would improve true molecular ions recovery.
237 279
238 The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data. 280 The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data.
239 281
240 282
241 283
242 284
243 ----------------- 285 -----------------
248 **Upstream tools** 290 **Upstream tools**
249 291
250 ========================= ========================================== ======= ========== 292 ========================= ========================================== ======= ==========
251 Name Output file Format Parameter 293 Name Output file Format Parameter
252 ========================= ========================================== ======= ========== 294 ========================= ========================================== ======= ==========
253 xcms.annotate xset.annotate_POS (or NEG).RData RData RData file 295 xcms.annotate xset.annotate_POS (or NEG).RData RData RData file
254 ========================= ========================================== ======= ========== 296 ========================= ========================================== ======= ==========
255 297
256 298
257 **General schema of the metabolomic workflow** 299 **General schema of the metabolomic workflow**
258 300
259 .. image:: probmetab_workflow.png 301 .. image:: probmetab_workflow.png
260 302
293 335
294 Samples to be excluded of peak counting to non-annotated peak selection. 336 Samples to be excluded of peak counting to non-annotated peak selection.
295 337
296 **Calculate** 338 **Calculate**
297 339
298 **intervals** 340 **intervals**
299 A vector of SNR numerical intervals, to which different carbon offset should be added to predicted C-number. 341 A vector of SNR numerical intervals, to which different carbon offset should be added to predicted C-number.
300 342
301 **offset** 343 **offset**
302 344
303 A vector of empirically estimated carbon offset to be added to predicted C-number. 345 A vector of empirically estimated carbon offset to be added to predicted C-number.
307 349
308 **likelihood** 350 **likelihood**
309 351
310 Which noise model to use, "erfc" to complementary error function, or "gaussian" to standard gaussian with two sd corresponding to the given p.p.m precision. 352 Which noise model to use, "erfc" to complementary error function, or "gaussian" to standard gaussian with two sd corresponding to the given p.p.m precision.
311 353
312 **precision** 354 **precision**
313 355
314 Equipment mass accuracy, usually the same used in exact mass search. 356 Equipment mass accuracy, usually the same used in exact mass search.
315 357
316 **KEGG database** 358 **KEGG database**
317 359
382 --------------------------------------------------- 424 ---------------------------------------------------
383 425
384 Changelog/News 426 Changelog/News
385 -------------- 427 --------------
386 428
429 **Version 1.1.0 - 06/04/2017**
430
431 - IMPROVEMENT: add some sections within to separate the different parts of the process
432
433 - IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet
434
387 **Version 1.0.1 - 16/05/2016** 435 **Version 1.0.1 - 16/05/2016**
388 436
389 - TEST: refactoring to pass planemo test using conda dependencies 437 - TEST: refactoring to pass planemo test using conda dependencies
390 438
391 439
392 **Version 1.0.0 - 10/06/2015** 440 **Version 1.0.0 - 10/06/2015**
393 441
394 - NEW: ProbMetab first version 442 - NEW: ProbMetab first version
395 443
396 444
397 </help> 445 </help>
398 446
399 <expand macro="citation" /> 447 <expand macro="citation" />
400 </tool> 448 </tool>
401
402