diff fasta_cli.xml @ 50:f2f4695ad996 draft

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

--- a/fasta_cli.xml	Wed Jan 20 13:28:34 2021 +0000
+++ b/fasta_cli.xml	Tue Mar 16 15:11:10 2021 +0000
@@ -1,4 +1,8 @@
-<tool id="fasta_cli" name="FastaCLI" version="1.0.1">
+<tool id="fasta_cli"
+      name="FastaCLI"
+      version="1.0.1"
+      profile="20.01"
+>
     <description>
         Appends decoy sequences to FASTA files
     </description>
@@ -11,7 +15,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set $temp_stderr = "fasta_cli_stderr"
         #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
 
         mkdir output &&
@@ -25,9 +28,8 @@
         ###########################################
 
         echo 'Creating decoy database.' &&
-        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag 2>> $temp_stderr &&
-        mv '${output_db_name}' output &&
-        cat $temp_stderr 2>&1;
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag &&
+        mv '${output_db_name}' output
 ]]>
     </command>
     <inputs>