Mercurial > repos > galaxyp > openms_rtevaluation
comparison RTEvaluation.xml @ 9:0cf2a9047a17 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:24:40 +0000 |
parents | 07dfbd60b100 |
children | b08e0ac606a4 |
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8:e782059156a0 | 9:0cf2a9047a17 |
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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> |