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comparison RTEvaluation.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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equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="RTEvaluation" name="RTEvaluation" 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>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="RTEvaluation" name="RTEvaluation" version="2.0.0">
5 <token name="@EXECUTABLE@">RTEvaluation</token> 5 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">RTEvaluation</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>RTEvaluation 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RTEvaluation
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -sequences_file ${param_sequences_file} 17 #end if
15 ${param_latex} 18 #if $param_out:
16 -p_value_dim_1 ${param_p_value_dim_1} 19 -out $param_out
17 -p_value_dim_2 ${param_p_value_dim_2} 20 #end if
18 -threads \${GALAXY_SLOTS:-24} 21 #if $param_sequences_file:
22 -sequences_file $param_sequences_file
23 #end if
24 #if $param_latex:
25 -latex
26 #end if
27 #if $param_p_value_dim_1:
28 -p_value_dim_1 $param_p_value_dim_1
29 #end if
30 #if $param_p_value_dim_2:
31 -p_value_dim_2 $param_p_value_dim_2
32 #end if
33 -threads \${GALAXY_SLOTS:-24}
34 #if $adv_opts.adv_opts_selector=='advanced':
35 #if $adv_opts.param_force:
36 -force
37 #end if
38 #end if
19 </command> 39 </command>
20 <inputs> 40 <inputs>
21 <param name="param_in" type="data" format="idXML" optional="False" label="input file" help="(-in)"/> 41 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
22 <param name="param_sequences_file" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are considered as false" help="(-sequences_file)"/> 42 <param format="fasta" help="(-sequences_file) &lt;br&gt;All peptides that are not a substring of a sequence in this file are considered as false" label="Filename of a FASTA file containing protein sequences" name="param_sequences_file" optional="True" type="data"/>
23 <param name="param_latex" type="boolean" truevalue="-latex true" falsevalue="-latex false" checked="false" optional="True" label="indicates whether the output file format of the table should be latex or csv" help="(-latex)"/> 43 <param checked="false" falsevalue="" help="(-latex) " label="indicates whether the output file format of the table should be latex or csv" name="param_latex" optional="True" truevalue="-latex" type="boolean"/>
24 <param name="param_p_value_dim_1" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Significance level of first dimension RT filter" help="(-p_value_dim_1)"/> 44 <param help="(-p_value_dim_1) " label="Significance level of first dimension RT filte" max="1.0" min="0.0" name="param_p_value_dim_1" optional="True" type="float" value="0.01"/>
25 <param name="param_p_value_dim_2" type="float" min="0.0" max="1.0" optional="True" value="0.05" label="Significance level of second dimension RT filter" help="(-p_value_dim_2)"/> 45 <param help="(-p_value_dim_2) " label="Significance level of second dimension RT filte" max="1.0" min="0.0" name="param_p_value_dim_2" optional="True" type="float" value="0.05"/>
26 </inputs> 46 <expand macro="advanced_options">
27 <outputs> 47 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
28 <data name="param_out" label="output file " format="tabular"/> 48 </expand>
29 </outputs> 49 </inputs>
30 <help>**What it does** 50 <outputs>
31 51 <data format="tabular" name="param_out"/>
32 Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. 52 </outputs>
53 <help>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
33 54
34 55
35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html 56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html</help>
36 57 </tool>
37 @REFERENCES@
38 </help>
39 </tool>