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comparison MapAlignmentEvaluation.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="1.12.0"> 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 <description>Evaluates alignment results against a ground truth.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.0.0">
5 <token name="@EXECUTABLE@">MapAlignmentEvaluation</token> 5 <description>Evaluates alignment results against a ground truth.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MapAlignmentEvaluation 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MapAlignmentEvaluation
11 14
12 -in ${param_in} 15 #if $param_in:
13 -gt ${param_gt} 16 -in $param_in
14 -type ${param_type} 17 #end if
15 -rt_dev ${param_rt_dev} 18 #if $param_gt:
16 -mz_dev ${param_mz_dev} 19 -gt $param_gt
17 -int_dev ${param_int_dev} 20 #end if
18 ${param_use_charge} 21 #if $param_type:
19 -threads \${GALAXY_SLOTS:-24} 22 -type
23 #if &quot; &quot; in str($param_type):
24 &quot;$param_type&quot;
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 -threads \${GALAXY_SLOTS:-24}
42 #if $adv_opts.adv_opts_selector=='advanced':
43 #if $adv_opts.param_force:
44 -force
45 #end if
46 #end if
47 &gt; $param_stdout
20 </command> 48 </command>
21 <inputs> 49 <inputs>
22 <param name="param_in" type="data" format="consensusXML" optional="False" label="input file: tool" help="(-in)"/> 50 <param format="consensusxml" help="(-in) " label="input file: tool" name="param_in" optional="False" type="data"/>
23 <param name="param_gt" type="data" format="consensusXML" optional="False" label="input file: ground truth" help="(-gt)"/> 51 <param format="consensusxml" help="(-gt) " label="input file: ground truth" name="param_gt" optional="False" type="data"/>
24 <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type)"> 52 <param help="(-type) " label="Caap Evaluation type" name="param_type" optional="False" type="select">
25 <option value="precision">precision</option> 53 <option value="precision">precision</option>
26 <option value="recall">recall</option> 54 <option value="recall">recall</option>
27 <option value="F1">F1</option> 55 <option value="F1">F1</option>
28 </param> 56 </param>
29 <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev)"/> 57 <param help="(-rt_dev) " label="Maximum allowed deviation of the retention time" name="param_rt_dev" type="float" value="0.1"/>
30 <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev)"/> 58 <param help="(-mz_dev) " label="Maximum allowed deviation of m/z" name="param_mz_dev" type="float" value="0.1"/>
31 <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev)"/> 59 <param help="(-int_dev) " label="Maximum allowed deviation of Intensity" name="param_int_dev" type="float" value="100.0"/>
32 <param name="param_use_charge" type="boolean" truevalue="-use_charge true" falsevalue="-use_charge false" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical." help="(-use_charge)"/> 60 <param checked="false" falsevalue="" help="(-use_charge) " label="Use charge criterion when assesing if two features are identical" name="param_use_charge" optional="True" truevalue="-use_charge" type="boolean"/>
33 </inputs> 61 <expand macro="advanced_options">
34 <outputs/> 62 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
35 <help>**What it does** 63 </expand>
36 64 </inputs>
37 Evaluates alignment results against a ground truth. 65 <outputs>
66 <data format="text" label="Output from stdout" name="param_stdout"/>
67 </outputs>
68 <help>Evaluates alignment results against a ground truth.
38 69
39 70
40 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html 71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html</help>
41 72 </tool>
42 @REFERENCES@
43 </help>
44 </tool>