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comparison DecoyDatabase.xml @ 0:bb36816527e8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 09:55:50 -0500
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children 112ff589ce35
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-1:000000000000 0:bb36816527e8
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.1.0">
5 <description>Create decoy peptide databases from normal ones.</description>
6 <macros>
7 <token name="@EXECUTABLE@">DecoyDatabase</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>DecoyDatabase
14
15 -in
16 #for token in $param_in:
17 $token
18 #end for
19 #if $param_out:
20 -out $param_out
21 #end if
22 #if $param_decoy_string:
23 -decoy_string "$param_decoy_string"
24 #end if
25 #if $param_decoy_string_position:
26 -decoy_string_position $param_decoy_string_position
27 #end if
28 #if $param_append:
29 -append $param_append
30 #end if
31 #if $param_method:
32 -method $param_method
33 #end if
34 #if $adv_opts.adv_opts_selector=='advanced':
35 #if $adv_opts.param_force:
36 -force
37 #end if
38 #end if
39 </command>
40 <inputs>
41 <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input FASTA file(s), each containing a database" help="(-in) It is recommended to include a contaminant database as well">
42 <sanitizer>
43 <valid initial="string.printable">
44 <remove value="'"/>
45 <remove value="&quot;"/>
46 </valid>
47 </sanitizer>
48 </param>
49 <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="(-decoy_string) ">
50 <sanitizer>
51 <valid initial="string.printable">
52 <remove value="'"/>
53 <remove value="&quot;"/>
54 </valid>
55 </sanitizer>
56 </param>
57 <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) ">
58 <option value="prefix" selected="true">prefix</option>
59 <option value="suffix">suffix</option>
60 </param>
61 <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) ">
62 <option value="true" selected="true">true</option>
63 <option value="false">false</option>
64 </param>
65 <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) ">
66 <option value="reverse" selected="true">reverse</option>
67 <option value="shuffle">shuffle</option>
68 </param>
69 <expand macro="advanced_options">
70 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
71 </expand>
72 </inputs>
73 <outputs>
74 <data name="param_out" format="fasta"/>
75 </outputs>
76
77 <tests>
78 <test>
79 <param name="param_in" value="DecoyDatabase_input.fasta"/>
80 <output name="param_out" file="DecoyDatabase_output.fasta"/>
81 </test>
82 </tests>
83
84 <help>Create decoy peptide databases from normal ones.
85
86
87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
88 </tool>