diff ident_params.xml @ 57:da885ca16cb2 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"

--- a/ident_params.xml	Wed Jan 20 13:29:07 2021 +0000
+++ b/ident_params.xml	Tue Mar 16 15:12:03 2021 +0000
@@ -1,4 +1,8 @@
-<tool id="ident_params" name="Identification Parameters" version="1.5.1">
+<tool id="ident_params"
+      name="Identification Parameters"
+      version="1.5.1"
+      profile="20.01"
+>
     <description>
         Sets the identification parameters to be used in SearchGUI and PeptideShaker apps
     </description>
@@ -12,7 +16,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set $temp_stderr = "searchgui_stderr"
         #set $bin_dir = "bin"
 
         mkdir output;
@@ -20,13 +23,12 @@
         export HOME=\$cwd;
 
 
-        echo "" > $temp_stderr &&
 
         echo 'running Identification Parameters CLI' &&
         #####################################################
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
-        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
+        searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
             --exec_dir="./bin/"
             -out './IdentificationParametersOutput.par'
 
@@ -614,10 +616,6 @@
             #end if
                 -fasta_target_decoy 0
                 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag
-
-        2> $temp_stderr) &&
-
-        cat $temp_stderr 2>&1;
 ]]>
     </command>
     <inputs>