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comparison DecoyDatabase.xml @ 3:2ff597ce7194 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 18:40:28 -0400
parents 112ff589ce35
children b9cd14affc81
comparison
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2:e1e2adf6209f 3:2ff597ce7194
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.1.0"> 4 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.2.0">
5 <description>Create decoy peptide databases from normal ones.</description> 5 <description>Create decoy protein DB from forward protein DB.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">DecoyDatabase</token> 7 <token name="@EXECUTABLE@">DecoyDatabase</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
28 "$param_decoy_string_position" 28 "$param_decoy_string_position"
29 #else 29 #else
30 $param_decoy_string_position 30 $param_decoy_string_position
31 #end if 31 #end if
32 #end if 32 #end if
33 #if $param_append: 33 #if $param_only_decoy:
34 -append 34 -only_decoy
35 #if " " in str($param_append):
36 "$param_append"
37 #else
38 $param_append
39 #end if
40 #end if 35 #end if
41 #if $param_method: 36 #if $param_method:
42 -method 37 -method
43 #if " " in str($param_method): 38 #if " " in str($param_method):
44 "$param_method" 39 "$param_method"
71 </param> 66 </param>
72 <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) "> 67 <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
73 <option value="prefix" selected="true">prefix</option> 68 <option value="prefix" selected="true">prefix</option>
74 <option value="suffix">suffix</option> 69 <option value="suffix">suffix</option>
75 </param> 70 </param>
76 <param name="param_append" display="radio" type="select" optional="False" value="true" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) "> 71 <param name="param_only_decoy" display="radio" type="boolean" truevalue="-only_decoy" falsevalue="" checked="false" optional="True" label="Write only decoy proteins to the output database instead of a combined database" help="(-only_decoy) "/>
77 <option value="true" selected="true">true</option>
78 <option value="false">false</option>
79 </param>
80 <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) "> 72 <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) ">
81 <option value="reverse" selected="true">reverse</option> 73 <option value="reverse" selected="true">reverse</option>
82 <option value="shuffle">shuffle</option> 74 <option value="shuffle">shuffle</option>
83 </param> 75 </param>
84 <expand macro="advanced_options"> 76 <expand macro="advanced_options">
92 <test> 84 <test>
93 <param name="param_in" value="DecoyDatabase_input.fasta"/> 85 <param name="param_in" value="DecoyDatabase_input.fasta"/>
94 <output name="param_out" file="DecoyDatabase_output.fasta"/> 86 <output name="param_out" file="DecoyDatabase_output.fasta"/>
95 </test> 87 </test>
96 </tests> 88 </tests>
97 <help>Create decoy peptide databases from normal ones. 89 <help>Create decoy protein DB from forward protein DB.
98 90
99 91
100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help> 92 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
101 </tool> 93 </tool>