Mercurial > repos > galaxyp > openms

comparison SeedListGenerator.xml @ 0:3070d71e0e5c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:3070d71e0e5c
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>