Mercurial > repos > galaxyp > peptideshaker
comparison ident_params.xml @ 57:da885ca16cb2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
author | galaxyp |
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date | Tue, 16 Mar 2021 15:12:03 +0000 |
parents | bb0130ff73ce |
children | 07ff622ec007 |
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56:1beff3ddce58 | 57:da885ca16cb2 |
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1 <tool id="ident_params" name="Identification Parameters" version="1.5.1"> | 1 <tool id="ident_params" |
2 name="Identification Parameters" | |
3 version="1.5.1" | |
4 profile="20.01" | |
5 > | |
2 <description> | 6 <description> |
3 Sets the identification parameters to be used in SearchGUI and PeptideShaker apps | 7 Sets the identification parameters to be used in SearchGUI and PeptideShaker apps |
4 </description> | 8 </description> |
5 <macros> | 9 <macros> |
6 <import>macros_basic.xml</import> | 10 <import>macros_basic.xml</import> |
10 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> | 14 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> |
11 </requirements> | 15 </requirements> |
12 <expand macro="stdio" /> | 16 <expand macro="stdio" /> |
13 <command> | 17 <command> |
14 <![CDATA[ | 18 <![CDATA[ |
15 #set $temp_stderr = "searchgui_stderr" | |
16 #set $bin_dir = "bin" | 19 #set $bin_dir = "bin" |
17 | 20 |
18 mkdir output; | 21 mkdir output; |
19 cwd=`pwd`; | 22 cwd=`pwd`; |
20 export HOME=\$cwd; | 23 export HOME=\$cwd; |
21 | 24 |
22 | 25 |
23 echo "" > $temp_stderr && | |
24 | 26 |
25 echo 'running Identification Parameters CLI' && | 27 echo 'running Identification Parameters CLI' && |
26 ##################################################### | 28 ##################################################### |
27 ## generate IdentificationParameters for SearchGUI ## | 29 ## generate IdentificationParameters for SearchGUI ## |
28 ##################################################### | 30 ##################################################### |
29 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI | 31 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI |
30 --exec_dir="./bin/" | 32 --exec_dir="./bin/" |
31 -out './IdentificationParametersOutput.par' | 33 -out './IdentificationParametersOutput.par' |
32 | 34 |
33 ## SPECTRUM MATCHING PARAMETERS | 35 ## SPECTRUM MATCHING PARAMETERS |
34 | 36 |
612 -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag | 614 -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag |
613 -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type | 615 -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type |
614 #end if | 616 #end if |
615 -fasta_target_decoy 0 | 617 -fasta_target_decoy 0 |
616 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag | 618 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag |
617 | |
618 2> $temp_stderr) && | |
619 | |
620 cat $temp_stderr 2>&1; | |
621 ]]> | 619 ]]> |
622 </command> | 620 </command> |
623 <inputs> | 621 <inputs> |
624 | 622 |
625 | 623 |