diff searchgui.xml @ 58:07ff622ec007 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"

--- 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>