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comparison RTEvaluation.xml @ 9:0cf2a9047a17 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:24:40 +0000
parents 07dfbd60b100
children b08e0ac606a4
comparison
equal deleted inserted replaced
8:e782059156a0 9:0cf2a9047a17
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="RTEvaluation" name="RTEvaluation" version="2.3.0"> 4 <tool id="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description> 5 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RTEvaluation</token> 7 <token name="@EXECUTABLE@">RTEvaluation</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[RTEvaluation 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 #if $sequences_file:
22 mkdir sequences_file &&
23 ln -s '$sequences_file' 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)' &&
17 #end if 24 #end if
18 #if $param_out: 25 mkdir out &&
19 -out $param_out 26
27 ## Main program call
28
29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in
34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
35 #if $sequences_file:
36 -sequences_file
37 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)'
20 #end if 38 #end if
21 #if $param_latex: 39 -out
22 -latex 40 'out/output.${gxy2omsext("csv")}'
23 #end if 41
24 #if $param_p_value_dim_1: 42 ## Postprocessing
25 -p_value_dim_1 $param_p_value_dim_1 43 && mv 'out/output.${gxy2omsext("csv")}' '$out'
26 #end if 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
27 #if $param_p_value_dim_2: 45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
28 -p_value_dim_2 $param_p_value_dim_2 46 #end if]]></command>
29 #end if 47 <configfiles>
30 #if $adv_opts.adv_opts_selector=='advanced': 48 <inputs name="args_json" data_style="paths"/>
31 #if $adv_opts.param_force: 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
32 -force 50 </configfiles>
33 #end if
34 #end if
35 ]]></command>
36 <inputs> 51 <inputs>
37 <param name="param_in" type="data" format="idxml" optional="False" label="Input file" help="(-in) "/> 52 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
38 <param name="param_latex" display="radio" type="boolean" truevalue="-latex" falsevalue="" checked="false" optional="True" label="Indicates whether the output file format of the table should be LaTeX or CSV (default)" help="(-latex) "/> 53 <param name="sequences_file" argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/>
39 <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 filte" help="(-p_value_dim_1) "/> 54 <param name="latex" argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or CSV (default)" help=""/>
40 <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 filte" help="(-p_value_dim_2) "/> 55 <param name="p_value_dim_1" argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/>
41 <expand macro="advanced_options"> 56 <param name="p_value_dim_2" argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/>
42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 57 <expand macro="adv_opts_macro">
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
60 <expand macro="list_string_san"/>
61 </param>
43 </expand> 62 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 </param>
44 </inputs> 66 </inputs>
45 <outputs> 67 <outputs>
46 <data name="param_out" format="tabular"/> 68 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data>
47 </outputs> 72 </outputs>
48 <help>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. 73 <tests>
74 <expand macro="autotest_RTEvaluation"/>
75 <expand macro="manutest_RTEvaluation"/>
76 </tests>
77 <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
49 78
50 79
51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_RTEvaluation.html</help> 80 For more information, visit http://www.openms.de/documentation/UTILS_RTEvaluation.html]]></help>
81 <expand macro="references"/>
52 </tool> 82 </tool>