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comparison ProbMetab.xml @ 5:1dd90aa7815d draft

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planemo upload commit f9da57d32476742b887a77435eb77c70494ccf96
author lecorguille
date Fri, 07 Apr 2017 03:31:35 -0400
parents a1b528cba999
children cbf292c32002
comparison
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4:a1b528cba999 5:1dd90aa7815d
39 ##image_pos $acquisition_options.input_mode.image_pos 39 ##image_pos $acquisition_options.input_mode.image_pos
40 #end if 40 #end if
41 41
42 #end if 42 #end if
43 43
44 #if $option_toexclude.option == "show": 44 ## Extraction of CAMERA annotation [get.annot]
45 toexclude $option_toexclude.toexclude 45 allowMiss $getannot.allowMiss
46 #if $getannot.option_toexclude.option == "show":
47 toexclude $getannot.option_toexclude.toexclude
46 #end if 48 #end if
47 allowMiss $allowMiss 49
48 html $html 50 ## Database matching [create.reactionM]
49 kegg_db $kegg_db 51 kegg_db $db.kegg_db
50 ppm_tol $ppm_tol 52 ppm_tol $db.ppm_tol
51 opt $opt 53
52 corths $corths 54 ## Probability calculations matrix export [export.class.table]
53 corprob $corprob 55 prob $export.prob
54 pcorprob $pcorprob 56 html $export.html
55 prob $prob 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
56 63
57 @COMMAND_LOG_EXIT@ 64 @COMMAND_LOG_EXIT@
58 65
59 </command> 66 </command>
60 67
78 <when value="show"> 85 <when value="show">
79 <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" />
80 </when> 87 </when>
81 </conditional> 88 </conditional>
82 --> 89 -->
90 <expand macro="input_file_load"/>
83 </when> 91 </when>
84 <!-- Two acquisition modes--> 92 <!-- Two acquisition modes-->
85 <when value="two"> 93 <when value="two">
86 <conditional name="input_mode"> 94 <conditional name="input_mode">
87 <param name="option" type="select" label="Choose your input type method:" > 95 <param name="option" type="select" label="Choose your input type method:" >
109 </when> 117 </when>
110 </conditional> 118 </conditional>
111 --> 119 -->
112 </when> 120 </when>
113 </conditional> 121 </conditional>
122 <expand macro="input_file_load" polarity="Positive"/>
123 <expand macro="input_file_load" polarity="Negative"/>
114 </when> 124 </when>
115 </conditional> 125 </conditional>
116 126
117 <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]." /> 127 <section name="getannot" title="Extraction of CAMERA annotation [get.annot]">
118 <conditional name="option_toexclude"> 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]." />
119 <param name="option" type="select" label="Exclude samples" > 129 <conditional name="option_toexclude">
120 <option value="show">show</option> 130 <param name="option" type="select" label="Exclude samples" >
121 <option value="hide" selected="true">hide</option> 131 <option value="show">show</option>
132 <option value="hide" selected="true">hide</option>
133 </param>
134 <when value="show">
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]" />
136 </when>
137 <when value="hide" />
138 </conditional>
139 </section>
140
141 <section name="db" title="Database matching [create.reactionM]">
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"/>
122 </param> 144 </param>
123 <when value="show"> 145 <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol]" />
124 <param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" /> 146 <!--
125 </when> 147 <conditional name="useIso_options">
126 <when value="hide" /> 148 <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" >
127 </conditional> 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]">
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]">
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
128 <!-- 183 <!--
129 <conditional name="useIso_options"> 184 <section name="cytoscape" title="CytoScape options">
130 <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).
131 <option value="show">Yes</option> 186 " />
132 <option value="hide" selected="true">No</option> 187 </section>
133 </param>
134 <when value="show">
135 <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." >
136 <option value="1">1</option>
137 <option value="2" selected="true">2</option>
138 </param>
139 </when>
140 </conditional>
141 --> 188 -->
142 <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
143
144 <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" >
145 <validator type="empty_field"/>
146 </param>
147 <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol] (create.reactionMfunction) " />
148
149 <param name="opt" type="select" label="Correlation option" help="[opt] (reac2cor function) cor for correlation, and pcor for partial correlation." >
150 <option value="cor" selected="true">cor</option>
151 <option value="pcor">pcor</option>
152 </param>
153
154 <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " />
155
156 <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob](reac2cor function)" />
157 <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths] (reac2cor function)" />
158
159 <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." >
160 <option value="count" selected="true">Count</option>
161 <option value="mean">Mean</option>
162 </param>
163 <!--
164 <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).
165 " />
166 -->
167
168 <expand macro="input_file_load"/>
169 <expand macro="input_file_load" polarity="Positive"/>
170 <expand macro="input_file_load" polarity="Negative"/>
171 </inputs> 190 </inputs>
172 191
173 <outputs> 192 <outputs>
174 <!-- <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" /> -->
175 <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" >
176 <filter>(html)</filter> 195 <filter>(export['html'])</filter>
177 </data> 196 </data>
178 <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" />
179 <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" >
180 <filter>(html)</filter> 199 <filter>(export['html'])</filter>
181 </data> 200 </data>
182 <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" />
183 <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" >
184 <filter>(drop_new-file_path['mode'] == 'one')</filter> 203 <filter>(acquisition_options['mode'] == 'one')</filter>
185 </data> 204 </data>
186 205
187 <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" >
188 <filter>(acquisition_options['mode'] == 'two')</filter> 207 <filter>(acquisition_options['mode'] == 'two')</filter>
189 </data> 208 </data>
200 <test> 219 <test>
201 <conditional name="acquisition_options"> 220 <conditional name="acquisition_options">
202 <param name="mode" value="one" /> 221 <param name="mode" value="one" />
203 <param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> 222 <param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
204 </conditional> 223 </conditional>
205 <param name="html" value="FALSE" /> 224 <expand macro="test_commun"/>
206 <expand macro="test_file_load_zip"/> 225 <expand macro="test_file_load_zip"/>
207 <assert_stdout> 226 <assert_stdout>
208 <has_text text="Step 1... determine cutoff point" /> 227 <has_text text="Step 1... determine cutoff point" />
209 <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" />
210 <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" />
214 <test> 233 <test>
215 <conditional name="acquisition_options"> 234 <conditional name="acquisition_options">
216 <param name="mode" value="one" /> 235 <param name="mode" value="one" />
217 <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> 236 <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
218 </conditional> 237 </conditional>
219 <param name="html" value="FALSE" /> 238 <expand macro="test_commun"/>
220 <expand macro="test_file_load_single"/> 239 <expand macro="test_file_load_single"/>
221 <assert_stdout> 240 <assert_stdout>
222 <has_text text="Step 1... determine cutoff point" /> 241 <has_text text="Step 1... determine cutoff point" />
223 <has_text text="Step 2... estimate parameters of null distribution and eta0" /> 242 <has_text text="Step 2... estimate parameters of null distribution and eta0" />
224 <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" /> 243 <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" />
405 --------------------------------------------------- 424 ---------------------------------------------------
406 425
407 Changelog/News 426 Changelog/News
408 -------------- 427 --------------
409 428
410 **Version 1.1.0 - 15/02/2017** 429 **Version 1.1.0 - 06/04/2017**
430
431 - IMPROVEMENT: add some sections within to separate the different parts of the process
411 432
412 - IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet 433 - IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet
413 434
414 **Version 1.0.1 - 16/05/2016** 435 **Version 1.0.1 - 16/05/2016**
415 436