|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="FFEval" name="FFEval" version="1.12.0">
|
|
|
3 <description>Evaluation tool for feature detection algorithms.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">FFEval</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>FFEval
|
|
|
11
|
|
|
12 -in ${param_in}
|
|
|
13 -truth ${param_truth}
|
|
|
14 -rt_tol ${param_rt_tol}
|
|
|
15 -rt_tol_abs ${param_rt_tol_abs}
|
|
|
16 -mz_tol ${param_mz_tol}
|
|
|
17 -out ${param_out}
|
|
|
18 -abort_reasons ${param_abort_reasons}
|
|
|
19 -out_roc ${param_out_roc}
|
|
|
20 -threads \${GALAXY_SLOTS:-24}
|
|
|
21 </command>
|
|
|
22 <inputs>
|
|
|
23 <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)"/>
|
|
|
24 <param name="param_truth" type="data" format="featureXML" optional="False" label="Truth feature file that defines what features should be found." help="(-truth)"/>
|
|
|
25 <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)"/>
|
|
|
26 <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)"/>
|
|
|
27 <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)"/>
|
|
|
28 <param name="param_abort_reasons" type="data" format="featureXML" optional="True" label="Feature file containing seeds with abort reasons." help="(-abort_reasons)"/>
|
|
|
29 </inputs>
|
|
|
30 <outputs>
|
|
|
31 <data name="param_out" label="Feature output file. If given, an annotated input file is written." format="featureXML"/>
|
|
|
32 <data name="param_out_roc" label="If given, a ROC curve file is created (ROC points based on intensity threshold)" format="tabular"/>
|
|
|
33 </outputs>
|
|
|
34 <help>**What it does**
|
|
|
35
|
|
|
36 Evaluation tool for feature detection algorithms.
|
|
|
37
|
|
|
38
|
|
|
39 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html
|
|
|
40
|
|
|
41 @REFERENCES@
|
|
|
42 </help>
|
|
|
43 </tool>
|
