Mercurial > repos > galaxyp > openms_openswathconfidencescoring

comparison OpenSwathConfidenceScoring.xml @ 0:70943f76cea6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:25:46 -0500
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children 2489199b7fa9
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-1:000000000000 0:70943f76cea6
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.1.0">
5 <description>Compute confidence scores for OpenSwath results</description>
6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathConfidenceScoring
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_lib:
19 -lib $param_lib
20 #end if
21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_trafo:
25 -trafo $param_trafo
26 #end if
27 #if $param_decoys:
28 -decoys $param_decoys
29 #end if
30 #if $param_transitions:
31 -transitions $param_transitions
32 #end if
33 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force:
35 -force
36 #end if
37 #if $adv_opts.param_GLM_intercept:
38 -GLM:intercept $adv_opts.param_GLM_intercept
39 #end if
40 #if $adv_opts.param_GLM_delta_rt:
41 -GLM:delta_rt $adv_opts.param_GLM_delta_rt
42 #end if
43 #if $adv_opts.param_GLM_dist_int:
44 -GLM:dist_int $adv_opts.param_GLM_dist_int
45 #end if
46 #end if
47 </command>
48 <inputs>
49 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file (OpenSwath results)" help="(-in) "/>
50 <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/>
51 <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/>
52 <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) "/>
53 <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) "/>
54 <expand macro="advanced_options">
55 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
56 <param name="param_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/>
57 <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/>
58 <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/>
59 </expand>
60 </inputs>
61 <outputs>
62 <data name="param_out" format="featurexml"/>
63 </outputs>
64 <help>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 </tool>