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comparison OpenSwathDIAPreScoring.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.0.0">
3 <description>Scoring spectra using the DIA scores.</description>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathDIAPreScoring
11
12 #if $param_tr:
13 -tr $param_tr
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 -swath_files
19 #for token in $param_swath_files:
20 $token
21 #end for
22 #if $param_min_upper_edge_dist:
23 -min_upper_edge_dist $param_min_upper_edge_dist
24 #end if
25 -threads \${GALAXY_SLOTS:-24}
26 #if $adv_opts.adv_opts_selector=='advanced':
27 #if $adv_opts.param_force:
28 -force
29 #end if
30 #end if
31 </command>
32 <inputs>
33 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
34 <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
35 <sanitizer>
36 <valid initial="string.printable">
37 <remove value="'"/>
38 <remove value="&quot;"/>
39 </valid>
40 </sanitizer>
41 </param>
42 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
43 <expand macro="advanced_options">
44 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
45 </expand>
46 </inputs>
47 <outputs>
48 <data name="param_out" format="tabular"/>
49 </outputs>
50 <help>**What it does**
51
52 Scoring spectra using the DIA scores.
53
54
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html</help>
56 <expand macro="references"/>
57 </tool>