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comparison maxquant.xml @ 15:41a49d4b2bc3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 80eb79844e82da22ce44a2ee9c9f202bed0b94d1
author galaxyp
date Fri, 22 Jul 2022 07:09:30 +0000
parents 1a3782e58489
children 6bb7ba55867a
comparison
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14:1a3782e58489 15:41a49d4b2bc3
382 <param name="mods_used_prot_quant" type="select" multiple="true" 382 <param name="mods_used_prot_quant" type="select" multiple="true"
383 label="Modifications used in protein quantification" 383 label="Modifications used in protein quantification"
384 help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ"> 384 help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ">
385 <expand macro="default_mod_option" value="Oxidation (M)"/> 385 <expand macro="default_mod_option" value="Oxidation (M)"/>
386 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> 386 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
387 <expand macro="mod_option" value="Carbamidomethyl (C)"/>
387 <expand macro="modification"/> 388 <expand macro="modification"/>
388 </param> 389 </param>
389 <!-- note: the following default is different to the mquant default --> 390 <!-- note: the following default is different to the mquant default -->
390 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true" 391 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
391 truevalue="True" falsevalue="False" 392 truevalue="True" falsevalue="False"
429 430
430 </section> 431 </section>
431 432
432 433
433 <repeat name="paramGroups" title="Parameter Group" min="1" default="1"> 434 <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
434 <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true" 435 <param type="data" format="thermo.raw,mzxml,mzml" name="files" label="Infiles" multiple="true"
435 help="Only select infiles matching the filetype specified in the input options."/> 436 help="Only select infiles matching the filetype specified in the input options."/>
436 <param type="integer" name="maxMissedCleavages" 437 <param type="integer" name="maxMissedCleavages"
437 label="missed cleavages" value="2" 438 label="missed cleavages" value="2"
438 help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/> 439 help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/>
439 <param name="fixedModifications" type="select" label="fixed modifications" 440 <param name="fixedModifications" type="select" label="fixed modifications"
440 multiple="true" 441 multiple="true"
441 help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid."> 442 help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid.">
443 <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
444 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
445 <expand macro="mod_option" value="Oxidation (M)"/>
442 <expand macro="modification"/> 446 <expand macro="modification"/>
443 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
444 </param> 447 </param>
445 <param name="variableModifications" type="select" label="variable modifications" 448 <param name="variableModifications" type="select" label="variable modifications"
446 multiple="true" 449 multiple="true"
447 help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels."> 450 help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels.">
451 <expand macro="mod_option" value="Carbamidomethyl (C)"/>
448 <expand macro="default_mod_option" value="Oxidation (M)"/> 452 <expand macro="default_mod_option" value="Oxidation (M)"/>
449 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/> 453 <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
450 <expand macro="modification"/> 454 <expand macro="modification"/>
451 </param> 455 </param>
452 <param name="enzymes" type="select" label="enzyme" 456 <param name="enzymes" type="select" label="enzyme"
453 multiple="true" 457 multiple="true"
454 help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search."> 458 help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search.">
1006 1010
1007 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too. 1011 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too.
1008 1012
1009 **Input files** 1013 **Input files**
1010 1014
1011 - Thermo raw, mzML, mzXMLfiles (in parameter group section) 1015 - Thermo raw, mzML, or mzXML files (in parameter group section)
1012 1016
1013 - The datatype of all files has to be either 'thermo.raw', 'mzML' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) 1017 - The datatype of all files has to be either 'thermo.raw', 'mzml' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
1014 - Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers: 1018 - Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:
1015 1019
1016 :: 1020 ::
1017 1021
1018 identifier parse rule description parse rule 1022 identifier parse rule description parse rule