Mercurial > repos > galaxyp > peptideshaker
diff fasta_cli.xml @ 57:da885ca16cb2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
| author | galaxyp |
|---|---|
| date | Tue, 16 Mar 2021 15:12:03 +0000 |
| parents | bb0130ff73ce |
| children | 07ff622ec007 |
line wrap: on
line diff
--- a/fasta_cli.xml Wed Jan 20 13:29:07 2021 +0000 +++ b/fasta_cli.xml Tue Mar 16 15:12:03 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>