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comparison searchgui.xml @ 48:64e3a8cc8ffb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 760ab8fdacac39fbebf1bfa3279e0156b48e164d
author galaxyp
date Thu, 27 Sep 2018 04:31:53 -0400
parents 44ca2967218c
children 58a3e6cb2598
comparison
equal deleted inserted replaced
47:44ca2967218c 48:64e3a8cc8ffb
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
2 <description> 2 <description>
3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
23 cwd=`pwd`; 23 cwd=`pwd`;
24 export HOME=\$cwd; 24 export HOME=\$cwd;
25 25
26 ## echo the search engines to run (single quotes important because X!Tandem) 26 ## echo the search engines to run (single quotes important because X!Tandem)
27 echo '$search_engines_options.engines'; 27 echo '$search_engines_options.engines';
28 echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}'; 28 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
29 29
30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present 30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
31 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties; 31 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
32 32
33 #for $mgf in $peak_lists: 33 #for $mgf in $peak_lists:
34 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf" 34 #set $input_name = $mgf.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
35 ln -s -f '${mgf}' '${input_name}'; 35 ln -s -f '${mgf}' '${input_name}';
36 #set $encoded_id = $__app__.security.encode_id($mgf.id) 36 #set $encoded_id = $__app__.security.encode_id($mgf.id)
37 echo 'Spectrums:${mgf.display_name}(API:${encoded_id})'; 37 echo 'Spectrums:${mgf.element_identifier}(API:${encoded_id})';
38 #end for 38 #end for
39 ##ln -s "${input_database}" input_database.fasta; 39 ##ln -s "${input_database}" input_database.fasta;
40 cp "${input_database}" input_database.fasta; 40 cp "${input_database}" input_database.fasta;
41 41
42 ########################################### 42 ###########################################