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comparison MapAlignmentEvaluation.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="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.0.0">
3 <description>Evaluates alignment results against a ground truth.</description>
4 <macros>
5 <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>MapAlignmentEvaluation
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_gt:
16 -gt $param_gt
17 #end if
18 #if $param_type:
19 -type
20 #if " " in str($param_type):
21 "$param_type"
22 #else
23 $param_type
24 #end if
25 #end if
26 #if $param_rt_dev:
27 -rt_dev $param_rt_dev
28 #end if
29 #if $param_mz_dev:
30 -mz_dev $param_mz_dev
31 #end if
32 #if $param_int_dev:
33 -int_dev $param_int_dev
34 #end if
35 #if $param_use_charge:
36 -use_charge
37 #end if
38 -threads \${GALAXY_SLOTS:-24}
39 #if $adv_opts.adv_opts_selector=='advanced':
40 #if $adv_opts.param_force:
41 -force
42 #end if
43 #end if
44 &gt; $param_stdout
45 </command>
46 <inputs>
47 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file: tool" help="(-in) "/>
48 <param name="param_gt" type="data" format="consensusxml" optional="False" label="input file: ground truth" help="(-gt) "/>
49 <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type) ">
50 <option value="precision">precision</option>
51 <option value="recall">recall</option>
52 <option value="F1">F1</option>
53 </param>
54 <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev) "/>
55 <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev) "/>
56 <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev) "/>
57 <param name="param_use_charge" type="boolean" truevalue="-use_charge" falsevalue="" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical" help="(-use_charge) "/>
58 <expand macro="advanced_options">
59 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
60 </expand>
61 </inputs>
62 <outputs>
63 <data name="param_stdout" format="text" label="Output from stdout"/>
64 </outputs>
65 <help>**What it does**
66
67 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 <expand macro="references"/>
72 </tool>