|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="SeedListGenerator" name="SeedListGenerator" version="2.0.0">
|
|
|
3 <description>Generates seed lists for feature detection.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">SeedListGenerator</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>SeedListGenerator
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15
|
|
|
16 #if $rep_param_out:
|
|
|
17 -out
|
|
|
18 #for token in $rep_param_out:
|
|
|
19 #if " " in str(token):
|
|
|
20 "$token.param_out"
|
|
|
21 #else
|
|
|
22 $token.param_out
|
|
|
23 #end if
|
|
|
24 #end for
|
|
|
25 #end if
|
|
|
26 #if $param_use_peptide_mass:
|
|
|
27 -use_peptide_mass
|
|
|
28 #end if
|
|
|
29 -threads \${GALAXY_SLOTS:-24}
|
|
|
30 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
31 #if $adv_opts.param_force:
|
|
|
32 -force
|
|
|
33 #end if
|
|
|
34 #end if
|
|
|
35 </command>
|
|
|
36 <inputs>
|
|
|
37 <param name="param_in" type="data" format="featurexml,consensusxml,mzml,idxml" optional="False" label="Input file (see below for details)" help="(-in) "/>
|
|
|
38 <param name="param_use_peptide_mass" type="boolean" truevalue="-use_peptide_mass" falsevalue="" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass) "/>
|
|
|
39 <expand macro="advanced_options">
|
|
|
40 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
41 </expand>
|
|
|
42 </inputs>
|
|
|
43 <outputs>
|
|
|
44 <data name="param_out" format="featurexml"/>
|
|
|
45 </outputs>
|
|
|
46 <help>**What it does**
|
|
|
47
|
|
|
48 Generates seed lists for feature detection.
|
|
|
49
|
|
|
50
|
|
|
51 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html</help>
|
|
|
52 <expand macro="references"/>
|
|
|
53 </tool>
|
