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comparison DecoyDatabase.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="DecoyDatabase" name="DecoyDatabase" version="1.12.0"> 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 <description>Create decoy peptide databases from normal ones.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.0.0">
5 <token name="@EXECUTABLE@">DecoyDatabase</token> 5 <description>Create decoy peptide databases from normal ones.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">DecoyDatabase</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>DecoyDatabase 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>DecoyDatabase
11 14
12 -in ${param_in} 15 -in
13 -out ${param_out} 16 #for token in $param_in:
14 -decoy_string ${param_decoy_string} 17 $token
15 -decoy_string_position ${param_decoy_string_position} 18 #end for
16 ${param_append} 19 #if $param_out:
17 ${param_shuffle} 20 -out $param_out
18 -threads \${GALAXY_SLOTS:-24} 21 #end if
22 #if $param_decoy_string:
23 -decoy_string &quot;$param_decoy_string&quot;
24 #end if
25 #if $param_decoy_string_position:
26 -decoy_string_position
27 #if &quot; &quot; in str($param_decoy_string_position):
28 &quot;$param_decoy_string_position&quot;
29 #else
30 $param_decoy_string_position
31 #end if
32 #end if
33 #if $param_append:
34 -append
35 #end if
36 #if $param_shuffle:
37 -shuffle
38 #end if
39 -threads \${GALAXY_SLOTS:-24}
40 #if $adv_opts.adv_opts_selector=='advanced':
41 #if $adv_opts.param_force:
42 -force
43 #end if
44 #end if
19 </command> 45 </command>
20 <inputs> 46 <inputs>
21 <param name="param_in" type="data" format="fasta" optional="False" size="20" label="Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well." help="(-in)"/> 47 <param format="fasta" help="(-in) It is recommended to include a contaminant database as well" label="Input FASTA file(s), each containing a database" multiple="true" name="param_in" optional="False" size="30" type="data">
22 <param name="param_decoy_string" type="text" size="20" value="_rev" label="String that is appended to the accession of the protein database to indicate a decoy protein." help="(-decoy_string)"/> 48 <sanitizer>
23 <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)"> 49 <valid initial="string.printable">
24 <option value="prefix">prefix</option> 50 <remove value="'"/>
25 <option value="suffix">suffix</option> 51 <remove value="&quot;"/>
26 </param> 52 </valid>
27 <param name="param_append" type="boolean" truevalue="-append true" falsevalue="-append false" 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)"/> 53 </sanitizer>
28 <param name="param_shuffle" type="boolean" truevalue="-shuffle true" falsevalue="-shuffle false" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle)"/> 54 </param>
29 </inputs> 55 <param help="(-decoy_string) " label="String that is appended to the accession of the protein database to indicate a decoy protein" name="param_decoy_string" size="30" type="text" value="_rev">
30 <outputs> 56 <sanitizer>
31 <data name="param_out" label="Output FASTA file where the decoy database will be written to." format="fasta"/> 57 <valid initial="string.printable">
32 </outputs> 58 <remove value="'"/>
33 <help>**What it does** 59 <remove value="&quot;"/>
34 60 </valid>
35 Create decoy peptide databases from normal ones. 61 </sanitizer>
62 </param>
63 <param help="(-decoy_string_position) " label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" name="param_decoy_string_position" optional="True" type="select" value="suffix">
64 <option value="prefix">prefix</option>
65 <option value="suffix">suffix</option>
66 </param>
67 <param checked="false" falsevalue="" help="(-append) " label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" name="param_append" optional="True" truevalue="-append" type="boolean"/>
68 <param checked="false" falsevalue="" help="(-shuffle) " label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" name="param_shuffle" optional="True" truevalue="-shuffle" type="boolean"/>
69 <expand macro="advanced_options">
70 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
71 </expand>
72 </inputs>
73 <outputs>
74 <data format="fasta" name="param_out"/>
75 </outputs>
76 <help>Create decoy peptide databases from normal ones.
36 77
37 78
38 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html 79 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
39 80 </tool>
40 @REFERENCES@
41 </help>
42 </tool>