# HG changeset patch # User galaxyp # Date 1591212741 0 # Node ID 710a80ad14f55d2a0432219672682650df26ea5f # Parent f2f79f0be7d17e911b632fc7d961ecc7893d2ec6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" diff -r f2f79f0be7d1 -r 710a80ad14f5 maxquant.xml --- a/maxquant.xml Mon Jun 01 15:50:52 2020 +0000 +++ b/maxquant.xml Wed Jun 03 19:32:21 2020 +0000 @@ -1,4 +1,4 @@ - + @@ -240,7 +240,7 @@ type="data" label="FASTA files" help="Specify one or more FASTA databases."/> + label="identifier parse rule" value=">([^\s]*)"> @@ -248,7 +248,7 @@ @@ -636,6 +636,8 @@ + + @@ -687,7 +689,25 @@ - Thermo raw, mzML, mzXMLfiles (in parameter group section) - 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) -- Fasta file: specify parse rules accordingly, default rules are compatible with uniprot +- Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers: + + :: + + identifier parse rule description parse rule + + Uniprot identifier >.*\|(.*)\| >.*\|.*\|[^ ]+ (.*) OS + + NCBI accession >(gi\|[0-9]*) + + IPI accession >IPI:([^\| .]*) + + Everything after '>' >(.*) + + Up to first space >([^ ]*) + + Up to first tab character >([^\t]*) + + - Optional files: - Tabular file with experimental design template: @@ -730,7 +750,7 @@ **Output files** -Different output file options are available, most of them are part of the MaxQuant txt directory. +Different output file options are available, most of them are part of the MaxQuant txt directory. ]]>