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comparison maxquant.xml @ 3:175e062b6a17 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
author galaxyp
date Thu, 15 Aug 2019 08:09:00 -0400
parents 8bac3cc5c5de
children dcd39bcc7481
comparison
equal deleted inserted replaced
2:666f3453a99d 3:175e062b6a17
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy1">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@VERSION@">maxquant</requirement> 6 <requirement type="package" version="@VERSION@">maxquant</requirement>
308 **Input files** 308 **Input files**
309 309
310 - Thermo raw file or mzXML file 310 - Thermo raw file or mzXML file
311 - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) 311 - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
312 - Optional files: 312 - Optional files:
313 - Tabular file with experimental design template: 313 - Tabular file with experimental design template:
314 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Fraction are abitrary strings, Experiment is an integer, PTM is either True or False. 314 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template:
315 315
316 :: 316 ::
317 317
318 Name Fraction Experiment PTM 318 Name Fraction Experiment PTM
319 File1 1 E1 False 319 File1 1 E1 False
320 File2 2 E1 False 320 File2 2 E1 False
321 ghost 234 none
321 File3 3 E1 False 322 File3 3 E1 False
322 ... 323 File4 E2 true
323 ... 324 File5 E1
325
326 - This is the counter-example with one error per line:
327
328 ::
329
330 Name Fraction Experiment PTM
331 File1 1 E1 no (wrong PTM value)
332 File2.mzxml 1 E2 (filename with extension)
333 File3 f3 E1 (fraction not an integer)
334 File4 1 (missing experiment)
335 (File5 misssing)
324 336
325 **Parameter Options** 337 **Parameter Options**
326 338
327 - Quantification options 339 - Quantification options
328 - label based: 340 - label based: