Mercurial > repos > galaxyp > peptideshaker

comparison fasta_cli.xml @ 57:da885ca16cb2 draft

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"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
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56:1beff3ddce58 57:da885ca16cb2
1 <tool id="fasta_cli" name="FastaCLI" version="1.0.1"> 1 <tool id="fasta_cli"
2 name="FastaCLI"
3 version="1.0.1"
4 profile="20.01"
5 >
2 <description> 6 <description>
3 Appends decoy sequences to FASTA files 7 Appends decoy sequences to FASTA files
4 </description> 8 </description>
5 <macros> 9 <macros>
6 <import>macros_basic.xml</import> 10 <import>macros_basic.xml</import>
9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> 13 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
10 </requirements> 14 </requirements>
11 <expand macro="stdio" /> 15 <expand macro="stdio" />
12 <command> 16 <command>
13 <![CDATA[ 17 <![CDATA[
14 #set $temp_stderr = "fasta_cli_stderr"
15 #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta" 18 #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
16 19
17 mkdir output && 20 mkdir output &&
18 cwd=`pwd` && 21 cwd=`pwd` &&
19 22
23 ########################################### 26 ###########################################
24 #### Creating decoy database #### 27 #### Creating decoy database ####
25 ########################################### 28 ###########################################
26 29
27 echo 'Creating decoy database.' && 30 echo 'Creating decoy database.' &&
28 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${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>> $temp_stderr && 31 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag &&
29 mv '${output_db_name}' output && 32 mv '${output_db_name}' output
30 cat $temp_stderr 2>&1;
31 ]]> 33 ]]>
32 </command> 34 </command>
33 <inputs> 35 <inputs>
34 <param format="fasta" name="input_database" type="data" label="Protein Database" 36 <param format="fasta" name="input_database" type="data" label="Protein Database"
35 help="Select FASTA database from history"/> 37 help="Select FASTA database from history"/>