Mercurial > repos > galaxyp > maxquant
comparison maxquant.xml @ 3:175e062b6a17 draft
"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 |
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| 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: |