comparison DecoyDatabase.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.0.0">
3 <description>Create decoy peptide databases from normal ones.</description>
4 <macros>
5 <token name="@EXECUTABLE@">DecoyDatabase</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>DecoyDatabase
11
12 -in
13 #for token in $param_in:
14 $token
15 #end for
16 #if $param_out:
17 -out $param_out
18 #end if
19 #if $param_decoy_string:
20 -decoy_string "$param_decoy_string"
21 #end if
22 #if $param_decoy_string_position:
23 -decoy_string_position
24 #if " " in str($param_decoy_string_position):
25 "$param_decoy_string_position"
26 #else
27 $param_decoy_string_position
28 #end if
29 #end if
30 #if $param_append:
31 -append
32 #end if
33 #if $param_shuffle:
34 -shuffle
35 #end if
36 -threads \${GALAXY_SLOTS:-24}
37 #if $adv_opts.adv_opts_selector=='advanced':
38 #if $adv_opts.param_force:
39 -force
40 #end if
41 #end if
42 </command>
43 <inputs>
44 <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">
45 <sanitizer>
46 <valid initial="string.printable">
47 <remove value="'"/>
48 <remove value="&quot;"/>
49 </valid>
50 </sanitizer>
51 </param>
52 <param name="param_decoy_string" type="text" size="30" value="_rev" label="String that is appended to the accession of the protein database to indicate a decoy protein" help="(-decoy_string) ">
53 <sanitizer>
54 <valid initial="string.printable">
55 <remove value="'"/>
56 <remove value="&quot;"/>
57 </valid>
58 </sanitizer>
59 </param>
60 <param name="param_decoy_string_position" type="select" optional="True" value="suffix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
61 <option value="prefix">prefix</option>
62 <option value="suffix">suffix</option>
63 </param>
64 <param name="param_append" type="boolean" truevalue="-append" falsevalue="" checked="false" optional="True" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) "/>
65 <param name="param_shuffle" type="boolean" truevalue="-shuffle" falsevalue="" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle) "/>
66 <expand macro="advanced_options">
67 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
68 </expand>
69 </inputs>
70 <outputs>
71 <data name="param_out" format="fasta"/>
72 </outputs>
73 <help>**What it does**
74
75 Create decoy peptide databases from normal ones.
76
77
78 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
79 <expand macro="references"/>
80 </tool>