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comparison maxquant.xml @ 8:ea0a1d50c83f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
author galaxyp
date Wed, 03 Jun 2020 15:32:53 -0400
parents d253b379322b
children f522c08e900c
comparison
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7:d253b379322b 8:ea0a1d50c83f
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy2"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy3">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter> 5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data> 6 </data>
238 </param> 238 </param>
239 <param format="fasta" multiple="true" name="fasta_files" 239 <param format="fasta" multiple="true" name="fasta_files"
240 type="data" label="FASTA files" 240 type="data" label="FASTA files"
241 help="Specify one or more FASTA databases."/> 241 help="Specify one or more FASTA databases."/>
242 <param name="identifier_parse_rule" type="text" 242 <param name="identifier_parse_rule" type="text"
243 label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$"> 243 label="identifier parse rule" value="&gt;([^\s]*)">
244 <sanitizer> 244 <sanitizer>
245 <valid initial="string.printable"> 245 <valid initial="string.printable">
246 <remove value="&apos;"/> 246 <remove value="&apos;"/>
247 </valid> 247 </valid>
248 </sanitizer> 248 </sanitizer>
249 </param> 249 </param>
250 <param name="description_parse_rule" type="text" 250 <param name="description_parse_rule" type="text"
251 label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" 251 label="description parse rule" value="&gt;(.*)"
252 help="Modify parse rules if needed."> 252 help="Modify parse rules if needed.">
253 <sanitizer> 253 <sanitizer>
254 <valid initial="string.printable"> 254 <valid initial="string.printable">
255 <remove value="&apos;"/> 255 <remove value="&apos;"/>
256 </valid> 256 </valid>
634 </test> 634 </test>
635 <!-- lfq, testing yaml conf file and mqpar.xml only --> 635 <!-- lfq, testing yaml conf file and mqpar.xml only -->
636 <test expect_num_outputs="2"> 636 <test expect_num_outputs="2">
637 <param name="ftype" value=".mzxml" /> 637 <param name="ftype" value=".mzxml" />
638 <param name="fasta_files" value="bsa.fasta" /> 638 <param name="fasta_files" value="bsa.fasta" />
639 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
640 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
639 <param name="min_unique_pep" value="1" /> 641 <param name="min_unique_pep" value="1" />
640 <param name="ibaq" value="True" /> 642 <param name="ibaq" value="True" />
641 <param name="ibaqLogFit" value="False" /> 643 <param name="ibaqLogFit" value="False" />
642 <repeat name="paramGroups"> 644 <repeat name="paramGroups">
643 <param name="files" value="BSA_min_22"/> 645 <param name="files" value="BSA_min_22"/>
685 **Input files** 687 **Input files**
686 688
687 - Thermo raw, mzML, mzXMLfiles (in parameter group section) 689 - Thermo raw, mzML, mzXMLfiles (in parameter group section)
688 690
689 - 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) 691 - 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)
690 - Fasta file: specify parse rules accordingly, default rules are compatible with uniprot 692 - Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:
693
694 ::
695
696 identifier parse rule description parse rule
697
698 Uniprot identifier >.*\|(.*)\| >.*\|.*\|[^ ]+ (.*) OS
699
700 NCBI accession >(gi\|[0-9]*)
701
702 IPI accession >IPI:([^\| .]*)
703
704 Everything after '>' >(.*)
705
706 Up to first space >([^ ]*)
707
708 Up to first tab character >([^\t]*)
709
710
691 - Optional files: 711 - Optional files:
692 712
693 - Tabular file with experimental design template: 713 - Tabular file with experimental design template:
694 714
695 - 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: 715 - 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:
728 - PTXQC quality control: quality control software creates an automatic quality control pdf report 748 - PTXQC quality control: quality control software creates an automatic quality control pdf report
729 749
730 750
731 **Output files** 751 **Output files**
732 752
733 Different output file options are available, most of them are part of the MaxQuant txt directory. 753 Different output file options are available, most of them are part of the MaxQuant txt directory.
734 ]]></help> 754 ]]></help>
735 <expand macro="citations"/> 755 <expand macro="citations"/>
736 </tool> 756 </tool>