Mercurial > repos > galaxyp > peptideshaker
diff searchgui.xml @ 58:07ff622ec007 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
author | galaxyp |
---|---|
date | Sat, 10 Apr 2021 15:57:17 +0000 |
parents | da885ca16cb2 |
children | 943a34df6047 |
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--- a/searchgui.xml Tue Mar 16 15:12:03 2021 +0000 +++ b/searchgui.xml Sat Apr 10 15:57:17 2021 +0000 @@ -170,7 +170,7 @@ <inputs> <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/> - <param format="fasta" name="input_fasta_file" type="data" label="Fasta file"/> + <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/> <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists" help="Select appropriate MGF/MZML dataset(s) from history" /> @@ -326,6 +326,21 @@ Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed. +**Input FASTA** + +In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences) +and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format: + + >generic[your tag]|[protein accession]|[protein description] + + or + + >generic[your tag]|[protein accession] + +See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta. + + + </help> <expand macro="citations" /> </tool>