Mercurial > repos > galaxyp > openms
comparison DecoyDatabase.xml @ 0:3070d71e0e5c draft
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author | bgruening |
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date | Thu, 16 Apr 2015 08:37:04 -0400 |
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-1:000000000000 | 0:3070d71e0e5c |
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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="""/> | |
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="""/> | |
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> |