comparison MapAlignmentEvaluation.xml @ 0:cf8a65bc9e8a draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:40:20 -0500
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-1:000000000000 0:cf8a65bc9e8a
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="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.1.0">
5 <description>Evaluates alignment results against a ground truth.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MapAlignmentEvaluation
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_gt:
19 -gt $param_gt
20 #end if
21 #if $param_type:
22 -type
23 #if " " in str($param_type):
24 "$param_type"
25 #else
26 $param_type
27 #end if
28 #end if
29 #if $param_rt_dev:
30 -rt_dev $param_rt_dev
31 #end if
32 #if $param_mz_dev:
33 -mz_dev $param_mz_dev
34 #end if
35 #if $param_int_dev:
36 -int_dev $param_int_dev
37 #end if
38 #if $param_use_charge:
39 -use_charge
40 #end if
41 #if $adv_opts.adv_opts_selector=='advanced':
42 #if $adv_opts.param_force:
43 -force
44 #end if
45 #end if
46 &gt; $param_stdout
47 </command>
48 <inputs>
49 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file: tool" help="(-in) "/>
50 <param name="param_gt" type="data" format="consensusxml" optional="False" label="input file: ground truth" help="(-gt) "/>
51 <param name="param_type" display="radio" type="select" optional="False" label="Caap Evaluation type" help="(-type) ">
52 <option value="precision">precision</option>
53 <option value="recall">recall</option>
54 <option value="F1">F1</option>
55 </param>
56 <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev) "/>
57 <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev) "/>
58 <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev) "/>
59 <param name="param_use_charge" display="radio" type="boolean" truevalue="-use_charge" falsevalue="" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical" help="(-use_charge) "/>
60 <expand macro="advanced_options">
61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
62 </expand>
63 </inputs>
64 <outputs>
65 <data name="param_stdout" format="text" label="Output from stdout"/>
66 </outputs>
67 <help>Evaluates alignment results against a ground truth.
68
69
70 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html</help>
71 </tool>