Mercurial > repos > galaxyp > peptideshaker
changeset 48:64e3a8cc8ffb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 760ab8fdacac39fbebf1bfa3279e0156b48e164d
| author | galaxyp |
|---|---|
| date | Thu, 27 Sep 2018 04:31:53 -0400 |
| parents | 44ca2967218c |
| children | 58a3e6cb2598 |
| files | searchgui.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/searchgui.xml Sat Sep 15 08:51:12 2018 -0400 +++ b/searchgui.xml Thu Sep 27 04:31:53 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -25,16 +25,16 @@ ## echo the search engines to run (single quotes important because X!Tandem) echo '$search_engines_options.engines'; - echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}'; + echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}'; ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties; #for $mgf in $peak_lists: - #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf" + #set $input_name = $mgf.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; #set $encoded_id = $__app__.security.encode_id($mgf.id) - echo 'Spectrums:${mgf.display_name}(API:${encoded_id})'; + echo 'Spectrums:${mgf.element_identifier}(API:${encoded_id})'; #end for ##ln -s "${input_database}" input_database.fasta; cp "${input_database}" input_database.fasta;