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comparison FFEval.xml @ 0:e3e4800c7bb6 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 10:01:45 -0500
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children 9e3d7a9185df
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-1:000000000000 0:e3e4800c7bb6
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: [Utilities]-->
4 <tool id="FFEval" name="FFEval" version="2.1.0">
5 <description>Evaluation tool for feature detection algorithms.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FFEval</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FFEval
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_truth:
19 -truth $param_truth
20 #end if
21 #if $param_rt_tol:
22 -rt_tol $param_rt_tol
23 #end if
24 #if $param_rt_tol_abs:
25 -rt_tol_abs $param_rt_tol_abs
26 #end if
27 #if $param_mz_tol:
28 -mz_tol $param_mz_tol
29 #end if
30 #if $param_out:
31 -out $param_out
32 #end if
33 #if $param_abort_reasons:
34 -abort_reasons $param_abort_reasons
35 #end if
36 #if $param_out_roc:
37 -out_roc $param_out_roc
38 #end if
39 #if $adv_opts.adv_opts_selector=='advanced':
40 #if $adv_opts.param_force:
41 -force
42 #end if
43 #end if
44 </command>
45 <inputs>
46 <param name="param_in" type="data" format="featurexml" optional="False" label="Feature input file, which contains the data to be tested against the truth file" help="(-in) "/>
47 <param name="param_truth" type="data" format="featurexml" optional="False" label="Truth feature file that defines what features should be found" help="(-truth) "/>
48 <param name="param_rt_tol" type="float" min="0.0" optional="True" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help="(-rt_tol) "/>
49 <param name="param_rt_tol_abs" type="float" min="-1.0" optional="True" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help="(-rt_tol_abs) "/>
50 <param name="param_mz_tol" type="float" min="0.0" optional="True" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help="(-mz_tol) "/>
51 <param name="param_abort_reasons" type="data" format="featurexml" optional="True" label="Feature file containing seeds with abort reasons" help="(-abort_reasons) "/>
52 <expand macro="advanced_options">
53 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
54 </expand>
55 </inputs>
56 <outputs>
57 <data name="param_out" format="featurexml"/>
58 <data name="param_out_roc" format="tabular"/>
59 </outputs>
60 <help>Evaluation tool for feature detection algorithms.
61
62
63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html</help>
64 </tool>