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comparison ProbMetab.xml @ 1:c4bd0c40eb3b draft

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planemo upload commit 1c73dd5ed7b5b8595963e0e1b6f8427978d8d5f5-dirty
author lecorguille
date Mon, 04 Jul 2016 09:51:51 -0400
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1 <tool id="Probmetab" name="ProbMetab Tool" version="1.0.1"> 1 <tool id="Probmetab" name="ProbMetab Tool" version="1.0.1">
2 2
3 <description>Wrapper function for ProbMetab R package.</description> 3 <description>Wrapper function for ProbMetab R package.</description>
4 4
5 <requirements> 5 <macros>
6 <requirement type="package" version="0.4_1">r-snow</requirement> 6 <import>macros.xml</import>
7 <requirement type="package" version="1.0">r-probmetab</requirement> 7 </macros>
8 <requirement type="package" version="1.1_4">r-batch</requirement> 8
9 </requirements> 9 <expand macro="requirements"/>
10 10 <expand macro="stdio"/>
11 <stdio>
12 <exit_code range="1:" level="fatal" />
13 </stdio>
14 11
15 <command> 12 <command>
16 LANG=C Rscript $__tool_directory__/probmetab.r 13 @COMMAND_CAMERA_SCRIPT@
17 #if $acquisition_options.mode == "one": 14 #if $acquisition_options.mode == "one":
18 mode_acquisition $acquisition_options.mode xa $acquisition_options.xa 15 mode_acquisition $acquisition_options.mode xa $acquisition_options.xa
19 ##if $acquisition_options.xsetnofill_options.option == "show": 16 ##if $acquisition_options.xsetnofill_options.option == "show":
20 ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill 17 ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill
21 ##end if 18 ##end if
37 toexclude $option_toexclude.toexclude 34 toexclude $option_toexclude.toexclude
38 #end if 35 #end if
39 allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol 36 allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol
40 opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob 37 opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob
41 38
42 #if $zip_file: 39 @COMMAND_ZIPFILE_LOAD@
43 zipfile $zip_file
44 #end if
45 40
46 </command> 41 </command>
47 42
48 <inputs> 43 <inputs>
49 44
159 <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). 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).
160 " /> 155 " />
161 156
162 --> 157 -->
163 158
164 <!-- To pass planemo test --> 159 <expand macro="zipfile_load"/>
165 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
166
167 </inputs> 160 </inputs>
168 161
169 <outputs> 162 <outputs>
170 <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> --> 163 <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> -->
171 <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" > 164 <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" >
195 188
196 <tests> 189 <tests>
197 <test> 190 <test>
198 <param name="acquisition_options|mode" value="one" /> 191 <param name="acquisition_options|mode" value="one" />
199 <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> 192 <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
200 <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> 193 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
194 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" />
201 <output name="log"> 195 <output name="log">
202 <assert_contents> 196 <assert_contents>
203 <has_text text="ko15 ko16 wt15 wt16" /> 197 <has_text text="ko15 ko16 wt15 wt16" />
204 <has_text text="Step 1... determine cutoff point" /> 198 <has_text text="Step 1... determine cutoff point" />
205 <has_text text="Step 2... estimate parameters of null distribution and eta0" /> 199 <has_text text="Step 2... estimate parameters of null distribution and eta0" />
211 </tests> 205 </tests>
212 206
213 207
214 <help> 208 <help>
215 209
216 .. class:: infomark 210 @HELP_AUTHORS@
217
218 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br
219
220 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics..
221 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/
222
223 .. class:: infomark
224
225 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff.
226
227 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
228
229 .. class:: infomark
230
231 **Contributors** Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr
232
233 ---------------------------------------------------
234
235 211
236 ========= 212 =========
237 ProbMetab 213 ProbMetab
238 ========= 214 =========
239 215
417 393
418 - NEW: ProbMetab first version 394 - NEW: ProbMetab first version
419 395
420 396
421 </help> 397 </help>
422 <citations> 398
423 <citation type="doi">10.1093/bioinformatics/btu019</citation> 399 <expand macro="citation" />
424 <citation type="doi">10.1093/bioinformatics/btu813</citation>
425 </citations>
426 </tool> 400 </tool>
427 401
428 402