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comparison OpenSwathConfidenceScoring.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="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.0.0">
3 <description>Compute confidence scores for OpenSwath results</description>
4 <macros>
5 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>OpenSwathConfidenceScoring
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_lib:
16 -lib $param_lib
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_trafo:
22 -trafo $param_trafo
23 #end if
24 #if $param_decoys:
25 -decoys $param_decoys
26 #end if
27 #if $param_transitions:
28 -transitions $param_transitions
29 #end if
30 -threads \${GALAXY_SLOTS:-24}
31 #if $adv_opts.adv_opts_selector=='advanced':
32 #if $adv_opts.param_force:
33 -force
34 #end if
35 #if $adv_opts.param_GLM_intercept:
36 -GLM:intercept $adv_opts.param_GLM_intercept
37 #end if
38 #if $adv_opts.param_GLM_delta_rt:
39 -GLM:delta_rt $adv_opts.param_GLM_delta_rt
40 #end if
41 #if $adv_opts.param_GLM_dist_int:
42 -GLM:dist_int $adv_opts.param_GLM_dist_int
43 #end if
44 #end if
45 </command>
46 <inputs>
47 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file (OpenSwath results)" help="(-in) "/>
48 <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/>
49 <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/>
50 <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys) "/>
51 <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help="(-transitions) "/>
52 <expand macro="advanced_options">
53 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
54 <param name="param_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/>
55 <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/>
56 <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/>
57 </expand>
58 </inputs>
59 <outputs>
60 <data name="param_out" format="featurexml"/>
61 </outputs>
62 <help>**What it does**
63
64 Compute confidence scores for OpenSwath results
65
66
67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html</help>
68 <expand macro="references"/>
69 </tool>