|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="SpecLibCreator" name="SpecLibCreator" version="2.0.0">
|
|
|
3 <description>Creates an MSP formatted spectral library.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">SpecLibCreator</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>SpecLibCreator
|
|
|
11
|
|
|
12 #if $param_info:
|
|
|
13 -info $param_info
|
|
|
14 #end if
|
|
|
15 #if $param_itemseperator:
|
|
|
16 -itemseperator "$param_itemseperator"
|
|
|
17 #end if
|
|
|
18 #if $param_itemenclosed:
|
|
|
19 -itemenclosed
|
|
|
20 #end if
|
|
|
21 #if $param_spec:
|
|
|
22 -spec $param_spec
|
|
|
23 #end if
|
|
|
24 #if $param_out:
|
|
|
25 -out $param_out
|
|
|
26 #end if
|
|
|
27 -threads \${GALAXY_SLOTS:-24}
|
|
|
28 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
29 #if $adv_opts.param_force:
|
|
|
30 -force
|
|
|
31 #end if
|
|
|
32 #end if
|
|
|
33 </command>
|
|
|
34 <inputs>
|
|
|
35 <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc" help="(-info) "/>
|
|
|
36 <param name="param_itemseperator" type="text" size="30" value="," label=" Seperator between items. e.g. ," help="(-itemseperator) ">
|
|
|
37 <sanitizer>
|
|
|
38 <valid initial="string.printable">
|
|
|
39 <remove value="'"/>
|
|
|
40 <remove value="""/>
|
|
|
41 </valid>
|
|
|
42 </sanitizer>
|
|
|
43 </param>
|
|
|
44 <param name="param_itemenclosed" type="boolean" truevalue="-itemenclosed" falsevalue="" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed" help="(-itemenclosed) e.g. '$peptide$,$run$"/>
|
|
|
45 <param name="param_spec" type="data" format="mzxml" optional="False" label="spectra" help="(-spec) "/>
|
|
|
46 <expand macro="advanced_options">
|
|
|
47 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
48 </expand>
|
|
|
49 </inputs>
|
|
|
50 <outputs>
|
|
|
51 <data name="param_out" format="msp"/>
|
|
|
52 </outputs>
|
|
|
53 <help>**What it does**
|
|
|
54
|
|
|
55 Creates an MSP formatted spectral library.
|
|
|
56
|
|
|
57
|
|
|
58 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html</help>
|
|
|
59 <expand macro="references"/>
|
|
|
60 </tool>
|
