Mercurial > repos > galaxyp > peptideshaker
diff searchgui.xml @ 52:864bd76db767 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
| author | galaxyp |
|---|---|
| date | Wed, 16 Jan 2019 08:18:39 -0500 |
| parents | 58a3e6cb2598 |
| children | bb0130ff73ce |
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--- a/searchgui.xml Mon Dec 31 02:20:36 2018 -0500 +++ b/searchgui.xml Wed Jan 16 08:18:39 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@"> +<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> @@ -23,7 +23,7 @@ cwd=`pwd`; export HOME=\$cwd; - echo "" > $temp_stderr && + echo "" > $temp_stderr && ## echo the search engines to run (single quotes important because X!Tandem) echo '$search_engines_options.engines'; @@ -46,8 +46,8 @@ ########################################### echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI - --exec_dir="\$cwd/${bin_dir}" - -temp_folder \$cwd + --exec_dir="\$cwd/${bin_dir}" + -temp_folder \$cwd -log \$cwd/searchgui.log 2>> $temp_stderr && ########################################### @@ -55,8 +55,8 @@ ########################################### #if $protein_database_options.create_decoy: echo 'Creating decoy database.' && - searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI - --exec_dir="\$cwd/${bin_dir}" + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI + --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy 2>> $temp_stderr && rm input_database.fasta && @@ -1128,8 +1128,8 @@ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> + <param name="fixed_modifications" value="Carbamidomethylation of C"/> + <param name="variable_modifications" value="Oxidation of M"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> @@ -1142,8 +1142,8 @@ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> + <param name="fixed_modifications" value="Carbamidomethylation of C"/> + <param name="variable_modifications" value="Oxidation of M"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/>