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comparison rmassbank.xml @ 2:94d6243033ec draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
author recetox
date Thu, 18 May 2023 13:00:47 +0000
parents 6fa3c0ba2e66
children
comparison
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1:6fa3c0ba2e66 2:94d6243033ec
1 <tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy2">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="creator"/> 5 <expand macro="creator"/>
6 6
13 </requirements> 13 </requirements>
14 <stdio> 14 <stdio>
15 <exit_code range="1:"/> 15 <exit_code range="1:"/>
16 <exit_code range=":-1"/> 16 <exit_code range=":-1"/>
17 </stdio> 17 </stdio>
18 <command><![CDATA[ 18 <command detect_errors="aggressive"><![CDATA[
19 #for $infile in $param_in: 19 #for $infile in $param_in:
20 ln -s '${infile}' '${infile.element_identifier}' && 20 ln -s '${infile}' '${infile.element_identifier}' &&
21 #end for 21 #end for
22 22
23 ln -s '${compounds}' '${compounds.element_identifier}' && 23 ln -s '${compounds}' '${compounds.element_identifier}' &&
206 <test> 206 <test>
207 <param name="compounds" value="compoundList.csv"/> 207 <param name="compounds" value="compoundList.csv"/>
208 <param name="infolist" value="infolist.csv"/> 208 <param name="infolist" value="infolist.csv"/>
209 <param name="mode" value="pH"/> 209 <param name="mode" value="pH"/>
210 <param name="param_in" value="1_3_Trifluoromethylphenyl_piperazin_2819_pos.mzML"/> 210 <param name="param_in" value="1_3_Trifluoromethylphenyl_piperazin_2819_pos.mzML"/>
211 <param name="rtMargin" value="0.4"/>
212 <param name="rtShift" value="0.0"/>
213 <param name="use_version" value="2"/>
214 <param name="use_rean_peaks" value="TRUE"/>
215 <param name="add_annotation" value="TRUE"/>
216 <param name="include_sp_tags" value="FALSE"/>
217 <param name="pH" value="0"/>
218 <param name="pM" value="16"/>
219 <param name="pNa" value="32"/>
220 <param name="mH" value="50"/>
221 <param name="mFA" value="66"/>
222 <param name="electronicNoiseWidth" value="0.3"/>
223 <param name="recalibrateBy" value="dppm"/>
224 <param name="recalibrateMS1" value="common"/>
225 <param name="recalibrateMS1Window" value="15"/>
226 <param name="multiplicityFilter" value="2"/>
227 <param name="ppmHighMass" value="10"/>
228 <param name="ppmLowMass" value="15"/>
229 <param name="massRangeDivision" value="120"/>
230 <param name="ppmFine" value="5"/> 211 <param name="ppmFine" value="5"/>
231 <param name="prelimCut" value="1000"/> 212
232 <param name="prelimCutRatio" value="0.0"/>
233 <param name="fineCut" value="0.0"/>
234 <param name="fineCutRatio" value="0.0"/>
235 <param name="specOkLimit" value="1000"/>
236 <param name="dbeMinLimit" value="-0.5"/>
237 <param name="satelliteMzLimit" value="0.5"/>
238 <param name="satelliteIntLimit" value="0.05"/>
239 <param name="ppmFine" value="5"/>
240 <param name="mzCoarse" value="0.5"/>
241 <param name="fillPrecursorScan" value="FALSE"/>
242 <param name="unknownMass" value="charged"/>
243 <output name="outputINI" value="mysettings_galaxy.ini" ftype="txt" lines_diff="2"/> 213 <output name="outputINI" value="mysettings_galaxy.ini" ftype="txt" lines_diff="2"/>
244 <output name="csvfile" value="failedPeaks.csv" ftype="csv" lines_diff="1"/> 214 <output name="csvfile" value="failedPeaks.csv" ftype="csv" lines_diff="1"/>
245 <output name="pdfplot" value="plot.pdf" compare="sim_size" delta_frac="0.1"/> 215 <output name="pdfplot" value="plot.pdf" compare="sim_size" delta_frac="0.1"/>
246 <output name="fllrdata" value="resultsFull.RData" compare="sim_size" delta_frac="0.1"/> 216 <output name="fllrdata" value="resultsFull.RData" compare="sim_size" delta_frac="0.1"/>
247 <output name="rafile" value="results_RA.RData" compare="sim_size" delta_frac="0.1"/> 217 <output name="rafile" value="results_RA.RData" compare="sim_size" delta_frac="0.1"/>
255 @HELP@ 225 @HELP@
256 ]]> 226 ]]>
257 </help> 227 </help>
258 228
259 <citations> 229 <citations>
260 <citation type="doi">https://onlinelibrary.wiley.com/doi/full/10.1002/jms.3131</citation> 230 <citation type="doi">10.1002/jms.3131</citation>
261 </citations> 231 </citations>
262 </tool> 232 </tool>
263