Mercurial > repos > galaxyp > openms_databasefilter
comparison DatabaseFilter.xml @ 0:a004cef51e2c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:27:13 -0400 |
parents | |
children | 3d430f968194 |
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-1:000000000000 | 0:a004cef51e2c |
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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="DatabaseFilter" name="DatabaseFilter" version="2.2.0"> | |
5 <description>Filters a protein database (FASTA format) based on identified proteins</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">DatabaseFilter</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="references"/> | |
11 <expand macro="stdio"/> | |
12 <expand macro="requirements"/> | |
13 <command>DatabaseFilter | |
14 | |
15 #if $param_in: | |
16 -in $param_in | |
17 #end if | |
18 #if $param_id: | |
19 -id $param_id | |
20 #end if | |
21 #if $param_method: | |
22 -method | |
23 #if " " in str($param_method): | |
24 "$param_method" | |
25 #else | |
26 $param_method | |
27 #end if | |
28 #end if | |
29 #if $param_out: | |
30 -out $param_out | |
31 #end if | |
32 #if $adv_opts.adv_opts_selector=='advanced': | |
33 #if $adv_opts.param_force: | |
34 -force | |
35 #end if | |
36 #end if | |
37 </command> | |
38 <inputs> | |
39 <param name="param_in" type="data" format="fasta" optional="False" label="Input FASTA file, containing a database" help="(-in) "/> | |
40 <param name="param_id" type="data" format="idxml,mzid" optional="False" label="Input file containing identified peptides and proteins" help="(-id) "/> | |
41 <param name="param_method" display="radio" type="select" optional="False" value="whitelist" label="Switch between white-/blacklisting" help="(-method) "> | |
42 <option value="whitelist" selected="true">whitelist</option> | |
43 <option value="blacklist">blacklist</option> | |
44 </param> | |
45 <expand macro="advanced_options"> | |
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
47 </expand> | |
48 </inputs> | |
49 <outputs> | |
50 <data name="param_out" format="fasta"/> | |
51 </outputs> | |
52 <help>Filters a protein database (FASTA format) based on identified proteins | |
53 | |
54 | |
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DatabaseFilter.html</help> | |
56 </tool> |