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comparison abims_CAMERA_annotateDiffreport.xml @ 13:1c30ff90f3ae draft

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planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
author lecorguille
date Fri, 07 Apr 2017 07:42:18 -0400
parents 8dd6f0ffa763
children 225cb8347572
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12:9c037181588e 13:1c30ff90f3ae
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5"> 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.0">
2 2
3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</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_CAMERA_SCRIPT@ 13 @COMMAND_CAMERA_SCRIPT@
14 xfunction annotatediff 14 xfunction annotatediff
15 image $image 15 image '$image'
16 16
17 variableMetadataOutput $variableMetadata
18 dataMatrixOutput $datamatrix
19 xsetRdataOutput $rdata
20
21 convert_param $convert_param num_digits $num_digits
22 nSlaves \${GALAXY_SLOTS:-1} 17 nSlaves \${GALAXY_SLOTS:-1}
23 sigma $sigma perfwhm $perfwhm 18
24 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac 19 ## output
25 ppm $ppm mzabs $mzabs intval $intval 20 variableMetadataOutput '$variableMetadata'
26 max_peaks $max_peaks 21 dataMatrixOutput '$datamatrix'
22
23 ## groupFWHM
24 sigma $groupfwhm.sigma
25 perfwhm $groupfwhm.perfwhm
26
27 ## findGeneral
28 ppm $findgeneral.ppm
29 mzabs $findgeneral.mzabs
30
31 ## findIsotopes
32 maxcharge $findisotopes.maxcharge
33 maxiso $findisotopes.maxiso
34 minfrac $findisotopes.minfrac
35
27 quick $quick_block.quick 36 quick $quick_block.quick
28 #if $quick_block.quick == "FALSE" 37 #if $quick_block.quick == "FALSE":
29 polarity $quick_block.polarity 38 xsetRdataOutput '$rdata_quick_false'
30 cor_eic_th $quick_block.cor_eic_th 39
31 graphMethod $quick_block.graphMethod 40 ## groupcorr
32 pval $quick_block.pval 41 cor_eic_th $quick_block.groupcorr.cor_eic_th
33 calcCiS $quick_block.calcCiS 42 graphMethod $quick_block.groupcorr.graphMethod
34 calcIso $quick_block.calcIso 43 pval $quick_block.groupcorr.pval
35 calcCaS $quick_block.calcCaS 44 calcCiS $quick_block.groupcorr.calcCiS
36 multiplier $quick_block.multiplier 45 calcIso $quick_block.groupcorr.calcIso
46 calcCaS $quick_block.groupcorr.calcCaS
47
48 ## findadducts
49 polarity $quick_block.findadducts.polarity
50 max_peaks $quick_block.findadducts.max_peaks
51 #if $quick_block.findadducts.rules_block.rules_select == "FALSE":
52 multiplier $quick_block.findadducts.rules_block.multiplier
53 #else
54 rules $quick_block.findadducts.rules_block.rules
55 #end if
56 #else
57 xsetRdataOutput '$rdata_quick_true'
37 #end if 58 #end if
38 59
39 #if $options.option == "show": 60 #if $diffreport.options.option == "show":
61 ## diffreport
40 runDiffreport TRUE 62 runDiffreport TRUE
41 eicmax $options.eicmax 63 eicmax $diffreport.options.eicmax
42 eicwidth $options.eicwidth 64 eicwidth $diffreport.options.eicwidth
43 value $options.value 65 value $diffreport.options.value
44 sortpval $options.sortpval 66 sortpval $diffreport.options.sortpval
45 h $options.h 67 h $diffreport.options.h
46 w $options.w 68 w $diffreport.options.w
47 mzdec $options.mzdec 69 mzdec $diffreport.options.mzdec
48 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
49 #end if 70 #end if
50 71
51 @COMMAND_ZIPFILE_LOAD@ 72 @COMMAND_PEAKLIST@
73
74 @COMMAND_FILE_LOAD@
52 75
53 ]]></command> 76 ]]></command>
54 77
55 <inputs> 78 <inputs>
56 79
57 80
58 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> 81 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />
59 82
60 <param name="convert_param" 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"/> 83 <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]" expanded="True">
61 <param name="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" /> 84 <param name="sigma" type="integer" value="6" label="Multiplier of the standard deviation" help="[sigma]" />
62 85 <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="Percentage of FWHM width" help="[perfwhm]" />
63 <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" /> 86 </section>
64 <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" /> 87
65 <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" /> 88 <section name="findgeneral" title="Annotation general options" expanded="True">
66 <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" /> 89 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />
67 <param name="minfrac" type="float" value="0.5" max="1" min="0" label="findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" /> 90 <param name="mzabs" type="float" value="0.015" label="General absolut error in m/z" help="[mzabs]" />
68 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" /> 91 </section>
69 <param name="mzabs" type="float" value="0.015" label="mzabs" help="General absolut error in m/z" /> 92
70 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below"> 93 <section name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True">
71 <option value="into" selected="true">into</option> 94 <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" />
72 <option value="maxo" >maxo</option> 95 <param name="maxiso" type="integer" value="4" label="Max. number of expected isotopes" help="[maxiso]" />
73 <option value="intb">intb</option> 96 <param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" />
74 </param> 97 </section>
75 98
76
77 <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" />
78 <conditional name="quick_block"> 99 <conditional name="quick_block">
79 <param name="quick" type="select" label="Quick mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts"> 100 <param name="quick" type="select" label="Mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts">
80 <option value="TRUE">TRUE</option> 101 <option value="FALSE" selected="true">All functions</option>
81 <option value="FALSE" selected="true">FALSE</option> 102 <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option>
82 </param> 103 </param>
83 <when value="FALSE"> 104 <when value="FALSE">
84 <param name="polarity" type="select" label="findAdducts: Which polarity mode was used for measuring of the ms sample" help="polarity"> 105
85 <option value="positive" >positive</option> 106 <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True">
86 <option value="negative" selected="true">negative</option> 107 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" />
87 </param> 108 <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]">
88 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" /> 109 <option value="hcs" selected="true">hcs</option>
89 <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]"> 110 <option value="lpc">lpc</option>
90 <option value="hcs" selected="true">hcs</option> 111 </param>
91 <option value="lpc">lpc</option> 112 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" />
92 </param> 113 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/>
93 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" /> 114 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
94 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> 115 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/>
95 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> 116 </section>
96 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> 117
97 <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> 118 <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True">
98 </when> 119 <param name="polarity" type="select" label="Which polarity mode was used for measuring of the ms sample" help="polarity">
99 <when value="TRUE"> 120 <option value="positive" >positive</option>
121 <option value="negative" selected="true">negative</option>
122 </param>
123 <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" />
124 <conditional name="rules_block">
125 <param name="rules_select" type="select" label="Use a personal ruleset file">
126 <option value="TRUE">TRUE</option>
127 <option value="FALSE" selected="true">FALSE</option>
128 </param>
129 <when value="FALSE">
130 <param name="multiplier" type="integer" value="3" label="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" />
131 </when>
132 <when value="TRUE">
133 <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" />
134 </when>
135 </conditional>
136 </section>
137
138 </when>
139 <when value="TRUE">
100 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> 140 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
101 </when>
102 </conditional>
103
104
105 <!-- Annotatediffreport specific parameters -->
106 <conditional name="options">
107 <param name="option" type="select" label="Number of condition">
108 <option value="hide" selected="true">One condition</option>
109 <option value="show">Two or more conditions</option>
110 </param>
111 <when value="show">
112 <param name="eicmax" type="integer" value="0" label="diffreport: number of the most significantly different analytes to create EICs for" help="[eicmax]" />
113 <param name="eicwidth" type="integer" value="200" label="diffreport: width (in seconds) of EICs produced" help="[eicwidth]" />
114 <param name="value" type="select" label="diffreport: Intensity values to be used for the diffreport" help="[value]">
115 <option value="into" selected="true">into</option>
116 <option value="maxo" >maxo</option>
117 <option value="intb">intb</option>
118 </param>
119 <param name="h" type="integer" value="480" label="diffreport: Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" />
120 <param name="w" type="integer" value="640" label="diffreport: Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
121 <param name="mzdec" type="integer" value="2" label="diffreport: Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
122 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
123 </when>
124 <when value="hide">
125 </when> 141 </when>
126 </conditional> 142 </conditional>
127 143
128 <expand macro="zipfile_load"/> 144 <!-- Diffreport specific parameters -->
145 <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True">
146 <conditional name="options">
147 <param name="option" type="select" label="Number of condition">
148 <option value="hide" selected="true">One condition</option>
149 <option value="show">Two or more conditions</option>
150 </param>
151 <when value="show">
152 <param name="eicmax" type="integer" value="0" label="Number of the most significantly different analytes to create EICs for" help="[eicmax]" />
153 <param name="eicwidth" type="integer" value="200" label="Width (in seconds) of EICs produced" help="[eicwidth]" />
154 <param name="value" type="select" label="Intensity values to be used for the diffreport" help="[value]">
155 <option value="into" selected="true">into</option>
156 <option value="maxo" >maxo</option>
157 <option value="intb">intb</option>
158 </param>
159 <param name="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" />
160 <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
161 <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
162 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
163 </when>
164 <when value="hide">
165 </when>
166 </conditional>
167 </section>
168
169 <expand macro="input_peaklist"/>
170 <expand macro="input_file_load"/>
129 </inputs> 171 </inputs>
130 172
131 <outputs> 173 <outputs>
132 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> 174 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
133 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> 175 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
134 <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" > 176 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" >
177 <filter>quick_block['quick'] == 'FALSE'</filter>
135 <change_format> 178 <change_format>
136 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> 179 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
137 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> 180 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
138 </change_format> 181 </change_format>
139 </data> 182 </data>
140 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> 183 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" >
141 <filter>(options['option'] == 'show')</filter> 184 <filter>quick_block['quick'] == 'TRUE'</filter>
142 </data> 185 </data>
186 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true">
187 <filter>diffreport['options']['option'] == 'show'</filter>
188 <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" />
189 <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" />
190 </data>
143 </outputs> 191 </outputs>
144 192
145 <tests> 193 <tests>
146 <!--<test>
147 <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/>
148 <param name="convert_param" value="False"/>
149 <param name="num_digits" value="0"/>
150 <param name="sigma" value="6"/>
151 <param name="perfwhm" value="0.6"/>
152 <param name="maxcharge" value="3"/>
153 <param name="maxiso" value="4"/>
154 <param name="minfrac" value="0.5"/>
155 <param name="ppm" value="5"/>
156 <param name="mzabs" value="0.015"/>
157 <param name="intval" value="into"/>
158 <param name="max_peaks" value="100"/>
159 <param name="quick_block|quick" value="FALSE"/>
160 <param name="quick_block|polarity" value="negative"/>
161 <param name="quick_block|cor_eic_th" value="0.75"/>
162 <param name="quick_block|graphMethod" value="hcs"/>
163 <param name="quick_block|pval" value="0.05"/>
164 <param name="quick_block|calcCiS" value="True"/>
165 <param name="quick_block|calcIso" value="False"/>
166 <param name="quick_block|calcCaS" value="False"/>
167 <param name="quick_block|multiplier" value="3"/>
168 <param name="options|option" value="show"/>
169 <param name="options|eicmax" value="200"/>
170 <param name="options|eicwidth" value="200"/>
171 <param name="options|value" value="into"/>
172 <param name="options|h" value="480"/>
173 <param name="options|w" value="640"/>
174 <param name="options|mzdec" value="2"/>
175 <param name="options|sortpval" value="False"/>
176 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
177 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
178 <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
179 </test>-->
180 <test> 194 <test>
181 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> 195 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>
182 <param name="convert_param" value="False"/> 196 <expand macro="test_annotate_diffreport"/>
183 <param name="num_digits" value="0"/> 197 <expand macro="test_annotate_quick_true"/>
184 <param name="sigma" value="6"/> 198 <expand macro="test_file_load_zip"/>
185 <param name="perfwhm" value="0.6"/>
186 <param name="maxcharge" value="3"/>
187 <param name="maxiso" value="4"/>
188 <param name="minfrac" value="0.5"/>
189 <param name="ppm" value="5"/>
190 <param name="mzabs" value="0.015"/>
191 <param name="intval" value="into"/>
192 <param name="max_peaks" value="100"/>
193 <param name="quick_block|quick" value="FALSE"/>
194 <param name="quick_block|polarity" value="negative"/>
195 <param name="quick_block|cor_eic_th" value="0.75"/>
196 <param name="quick_block|graphMethod" value="hcs"/>
197 <param name="quick_block|pval" value="0.05"/>
198 <param name="quick_block|calcCiS" value="True"/>
199 <param name="quick_block|calcIso" value="False"/>
200 <param name="quick_block|calcCaS" value="False"/>
201 <param name="quick_block|multiplier" value="3"/>
202 <param name="options|option" value="show"/>
203 <param name="options|eicmax" value="200"/>
204 <param name="options|eicwidth" value="200"/>
205 <param name="options|value" value="into"/>
206 <param name="options|h" value="480"/>
207 <param name="options|w" value="640"/>
208 <param name="options|mzdec" value="2"/>
209 <param name="options|sortpval" value="False"/>
210 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
211 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" />
212 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> 199 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
213 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> 200 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
214 </test> 201 </test>
202 <test>
203 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
204 <expand macro="test_annotate_diffreport"/>
205 <expand macro="test_annotate_quick_true"/>
206 <expand macro="test_file_load_single"/>
207 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
208 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
209 </test>
210 <test>
211 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
212 <expand macro="test_annotate_diffreport"/>
213 <conditional name="quick_block">
214 <expand macro="test_annotate_quick_false" />
215 <section name="findadducts">
216 <param name="polarity" value="negative"/>
217 <conditional name="rules_block">
218 <param name="rules_select" value="TRUE"/>
219 <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/>
220 </conditional>
221 </section>
222 </conditional>
223 <expand macro="test_file_load_single"/>
224 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" />
225 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" />
226 </test>
215 </tests> 227 </tests>
216 228
217 229
218 230
219 <help><![CDATA[ 231 <help><![CDATA[
220 232
221 @HELP_AUTHORS@ 233 @HELP_AUTHORS@
222 234
223 ================ 235 ================
224 CAMERA.annotate 236 CAMERA.annotate
225 ================ 237 ================
237 CAMERA is designed to interact directly with processed peak data from the 249 CAMERA is designed to interact directly with processed peak data from the
238 R-package **xcms**. 250 R-package **xcms**.
239 251
240 **What it does?** 252 **What it does?**
241 253
242 The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable). 254 The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable).
243 255
244 If you have two or more conditions, it will return a diffreport result within the annotation results. 256 If you have two or more conditions, it will return a diffreport result within the annotation results.
245 The diffreport result shows the most significant differences between two sets of samples. Optionally 257 The diffreport result shows the most significant differences between two sets of samples. Optionally
246 create extracted ion chromatograms for the most significant differences. 258 create extracted ion chromatograms for the most significant differences.
247 259
263 **Downstream tools** 275 **Downstream tools**
264 276
265 +---------------------------+---------------------------------------+------------------------------------------------+ 277 +---------------------------+---------------------------------------+------------------------------------------------+
266 | Name | Output file | Format | 278 | Name | Output file | Format |
267 +===========================+=======================================+================================================+ 279 +===========================+=======================================+================================================+
268 |CAMERA_combinexsAnnot |xset.annotate.dataMatrix.tsv | rdata.camera.positive or rdata.camera.negative | 280 |CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative |
269 +---------------------------+---------------------------------------+------------------------------------------------+ 281 +---------------------------+---------------------------------------+------------------------------------------------+
270 |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular | 282 |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular |
271 +---------------------------+---------------------------------------+------------------------------------------------+ 283 +---------------------------+---------------------------------------+------------------------------------------------+
272 |Normalization Vdk/Lowess |xset.annotate.dataMatrix.tsv | Tabular | 284 |Normalization Vdk/Lowess |xset.annotate.dataMatrix.tsv | Tabular |
273 +---------------------------+---------------------------------------+------------------------------------------------+ 285 +---------------------------+---------------------------------------+------------------------------------------------+
301 +===========================+===========================+ 313 +===========================+===========================+
302 | 1 : RData file | rdata.xcms.fillpeaks | 314 | 1 : RData file | rdata.xcms.fillpeaks |
303 +---------------------------+---------------------------+ 315 +---------------------------+---------------------------+
304 316
305 317
318 [Optional] User defined ruleset:
319 --------------------------------
320
321 Example:
322
323 | "name","nmol","charge","massdiff","oidscore","quasi","ips"
324 | "[M-H]-",1,-1,-1.007276,1,1,1
325 | "[M-2H]2-",1,-2,-2.014552,2,0,1
326 | "[M-3H]3-",1,-3,-3.021828,3,0,1
327 | "[M-2H+Na]-",1,-1,20.974666,4,0,0.25
328 | "[M-H+Cl]2-",1,-2,33.962126,5,0,1
329 | "[M-2H+K]-",1,-1,36.948606,6,0,0.25
330 | "[M+Cl]-",1,-1,34.969402,7,1,1
331 | "[M+2Cl]2-",1,-2,69.938804,8,0,1
332 | "[2M-H]-",2,-1,-1.007276,1,0,0.5
333
306 ---------- 334 ----------
307 Parameters 335 Parameters
308 ---------- 336 ----------
309 337
310 diffreport: Intensity values to be used for the diffreport 338 diffreport: Intensity values to be used for the diffreport
326 | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup 354 | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup
327 355
328 xset.annotate.dataMatrix.tsv 356 xset.annotate.dataMatrix.tsv
329 357
330 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column). 358 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).
331 359
332 xset.annotate.zip 360 xset.annotate.zip
333 361
334 | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis). 362 | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).
335 363
336 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative 364 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative
337 365
338 | Rdata file, that be used outside Galaxy in R. 366 | Rdata file, that be used outside Galaxy in R.
339 367
340 ------ 368 ------
341 369
342 .. class:: infomark 370 .. class:: infomark
343 371
344 The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: 372 The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:
345 373
346 | Determine Vdk or Lowess (Data correction) 374 | Determine Vdk or Lowess (Data correction)
347 | Normalization Vdk/Lowess (Data correction) 375 | Normalization Vdk/Lowess (Data correction)
348 | Anova (Statistical analysis) 376 | Anova (Statistical analysis)
349 | PCA (Statistical analysis) 377 | PCA (Statistical analysis)
350 | Hierarchical Clustering (Statistical analysis) 378 | Hierarchical Clustering (Statistical analysis)
351 379
352 380
353 --------------------------------------------------- 381 ---------------------------------------------------
354 382
355 --------------- 383 ---------------
356 Working example 384 Working example
357 --------------- 385 ---------------
375 | Advanced options -> **hide** 403 | Advanced options -> **hide**
376 | Numver of condition -> Two or more conditioons 404 | Numver of condition -> Two or more conditioons
377 | eicmax -> **200** 405 | eicmax -> **200**
378 | eicwidth -> **200 (default)** 406 | eicwidth -> **200 (default)**
379 407
380 408
381 409
382 Output files 410 Output files
383 ------------ 411 ------------
384 412
385 **Example of an xset.annotate.dataMatrix.tsv output** 413 **Example of an xset.annotate.dataMatrix.tsv output**
386 414
387 .. image:: annotatediffreport_dataMatrix.png 415 .. image:: annotatediffreport_dataMatrix.png
388 416
389 **Example of a part of xset.annotate.variableMetadata.tsv output** 417 **Example of a part of xset.annotate.variableMetadata.tsv output**
390 418
391 .. image:: annotatediffreport_variableMetadata.png 419 .. image:: annotatediffreport_variableMetadata.png
392 420
393 421
394 --------------------------------------------------- 422 ---------------------------------------------------
395 423
396 Changelog/News 424 Changelog/News
397 -------------- 425 --------------
398 426
427 **Version 2.2.0 - 28/03/2017**
428
429 - BUGFIX: the diffreport ids didn't convert the rt in minute as the other export
430
431 - UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata.
432
433 - IMPROVEMENT: add some sections within to separate the different parts of the process
434
435 - IMPROVEMENT: add the possibility to use defined ruleset
436
437 - IMPROVEMENT: add the possibility to set the MZ digit within the identifiants
438
439 - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet
440
441
399 **Version 2.1.5 - 21/04/2016** 442 **Version 2.1.5 - 21/04/2016**
400 443
401 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 444 - UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0
402 445
403 446
404 **Version 2.1.4 - 18/04/2016** 447 **Version 2.1.4 - 18/04/2016**
405 448
406 - TEST: refactoring to pass planemo test using conda dependencies 449 - TEST: refactoring to pass planemo test using conda dependencies
415 - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf. 458 - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
416 459
417 - UPDATE: refactoring of internal management of inputs/outputs 460 - UPDATE: refactoring of internal management of inputs/outputs
418 461
419 462
420 VERSION 2.1.0 - 09/10/2015** 463 **VERSION 2.1.0 - 09/10/2015**
421 464
422 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) 465 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
423 466
424 467
425 VERSION 2.1.0 - 07/06/2015** 468 **VERSION 2.1.0 - 07/06/2015**
426 469
427 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. 470 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
428 471
429 - IMPROVEMENT: parameter labels have changed to facilitate their reading. 472 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
430 473
435 478
436 <expand macro="citation" /> 479 <expand macro="citation" />
437 480
438 481
439 </tool> 482 </tool>
440
441