Mercurial > repos > galaxyp > peptideshaker

comparison fasta_cli.xml @ 59:943a34df6047 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
author galaxyp
date Fri, 21 May 2021 19:13:14 +0000
parents 07ff622ec007
children 3ec27b4cee7c
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58:07ff622ec007 59:943a34df6047
26 ########################################### 26 ###########################################
27 #### Creating decoy database #### 27 #### Creating decoy database ####
28 ########################################### 28 ###########################################
29 29
30 echo 'Creating decoy database.' && 30 echo 'Creating decoy database.' &&
31 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 $database_processing_options.decoy_file_tag && 31 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
32 --exec_dir="./bin/"
33 -use_log_folder 0
34 -temp_folder `pwd`
35 -in '${input_database.display_name}'
36 -decoy
37 -decoy_flag $database_processing_options.decoy_tag
38 -suffix $database_processing_options.decoy_type
39 -decoy_suffix $database_processing_options.decoy_file_tag &&
32 mv '${output_db_name}' output 40 mv '${output_db_name}' output
33 ]]> 41 ]]>
34 </command> 42 </command>
35 <inputs> 43 <inputs>
36 <param format="fasta" name="input_database" type="data" label="Protein Database" 44 <param format="fasta" name="input_database" type="data" label="Protein Database"