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comparison FFEval.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="FFEval" name="FFEval" 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>Evaluation tool for feature detection algorithms.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="FFEval" name="FFEval" version="2.0.0">
5 <token name="@EXECUTABLE@">FFEval</token> 5 <description>Evaluation tool for feature detection algorithms.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FFEval</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FFEval 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FFEval
11 14
12 -in ${param_in} 15 #if $param_in:
13 -truth ${param_truth} 16 -in $param_in
14 -rt_tol ${param_rt_tol} 17 #end if
15 -rt_tol_abs ${param_rt_tol_abs} 18 #if $param_truth:
16 -mz_tol ${param_mz_tol} 19 -truth $param_truth
17 -out ${param_out} 20 #end if
18 -abort_reasons ${param_abort_reasons} 21 #if $param_rt_tol:
19 -out_roc ${param_out_roc} 22 -rt_tol $param_rt_tol
20 -threads \${GALAXY_SLOTS:-24} 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 -threads \${GALAXY_SLOTS:-24}
40 #if $adv_opts.adv_opts_selector=='advanced':
41 #if $adv_opts.param_force:
42 -force
43 #end if
44 #end if
21 </command> 45 </command>
22 <inputs> 46 <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)"/> 47 <param format="xml" help="(-in) " label="Feature input file, which contains the data to be tested against the truth file" name="param_in" optional="False" type="data"/>
24 <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 format="xml" help="(-truth) " label="Truth feature file that defines what features should be found" name="param_truth" optional="False" type="data"/>
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)"/> 49 <param help="(-rt_tol) " label="Allowed tolerance of RT relative to average feature RT span" min="0.0" name="param_rt_tol" optional="True" type="float" value="0.3"/>
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)"/> 50 <param help="(-rt_tol_abs) " label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" min="-1.0" name="param_rt_tol_abs" optional="True" type="float" value="-1.0"/>
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)"/> 51 <param help="(-mz_tol) " label="Allowed tolerance in m/z (is divided by charge)" min="0.0" name="param_mz_tol" optional="True" type="float" value="0.25"/>
28 <param name="param_abort_reasons" type="data" format="featureXML" optional="True" label="Feature file containing seeds with abort reasons." help="(-abort_reasons)"/> 52 <param format="xml" help="(-abort_reasons) " label="Feature file containing seeds with abort reasons" name="param_abort_reasons" optional="True" type="data"/>
29 </inputs> 53 <expand macro="advanced_options">
30 <outputs> 54 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
31 <data name="param_out" label="Feature output file. If given, an annotated input file is written." format="featureXML"/> 55 </expand>
32 <data name="param_out_roc" label="If given, a ROC curve file is created (ROC points based on intensity threshold)" format="tabular"/> 56 </inputs>
33 </outputs> 57 <outputs>
34 <help>**What it does** 58 <data format="xml" name="param_out"/>
35 59 <data format="tabular" name="param_out_roc"/>
36 Evaluation tool for feature detection algorithms. 60 </outputs>
61 <help>Evaluation tool for feature detection algorithms.
37 62
38 63
39 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html 64 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html</help>
40 65 </tool>
41 @REFERENCES@
42 </help>
43 </tool>