Mercurial > repos > galaxyp > openms_labeledeval

comparison LabeledEval.xml @ 14:785f5e8022a4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 22:37:38 +0000
parents 81b5149b41a9
children a501c0193c9c
comparison
equal deleted inserted replaced
13:81b5149b41a9 14:785f5e8022a4
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="LabeledEval" name="LabeledEval" version="2.3.0"> 4 <tool id="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description> Evaluation tool for isotope-labeled quantitation experiments.</description> 5 <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">LabeledEval</token> 7 <token name="@EXECUTABLE@">LabeledEval</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[LabeledEval 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_truth: 21 mkdir truth &&
19 -truth $param_truth 22 ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
20 #end if 23
21 #if $param_rt_tol: 24 ## Main program call
22 -rt_tol $param_rt_tol 25
23 #end if 26 set -o pipefail &&
24 #if $param_mz_tol: 27 @EXECUTABLE@ -write_ctd ./ &&
25 -mz_tol $param_mz_tol 28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
26 #end if 29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
27 #if $adv_opts.adv_opts_selector=='advanced': 30 -in
28 #if $adv_opts.param_force: 31 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
29 -force 32 -truth
30 #end if 33 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
31 #end if 34 | tee '$stdout'
32 &gt; $param_stdout 35
33 ]]></command> 36 ## Postprocessing
37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 && mv '@EXECUTABLE@.ctd' '$ctd_out'
39 #end if]]></command>
40 <configfiles>
41 <inputs name="args_json" data_style="paths"/>
42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 </configfiles>
34 <inputs> 44 <inputs>
35 <param name="param_in" type="data" format="featurexml" optional="False" label="Feature result file" help="(-in) "/> 45 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/>
36 <param name="param_truth" type="data" format="consensusxml" optional="False" label="Expected result file" help="(-truth) "/> 46 <param name="truth" argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/>
37 <param name="param_rt_tol" type="float" value="20.0" label="Maximum allowed retention time deviation" help="(-rt_tol) "/> 47 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/>
38 <param name="param_mz_tol" type="float" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help="(-mz_tol) "/> 48 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/>
39 <expand macro="advanced_options"> 49 <expand macro="adv_opts_macro">
40 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 50 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
51 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
52 <expand macro="list_string_san"/>
53 </param>
41 </expand> 54 </expand>
55 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
57 </param>
42 </inputs> 58 </inputs>
43 <outputs> 59 <outputs>
44 <data name="param_stdout" format="txt" label="Output from stdout"/> 60 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
61 <filter>OPTIONAL_OUTPUTS is None</filter>
62 </data>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data>
45 </outputs> 66 </outputs>
46 <help> Evaluation tool for isotope-labeled quantitation experiments. 67 <tests>
68 <expand macro="autotest_LabeledEval"/>
69 <expand macro="manutest_LabeledEval"/>
70 </tests>
71 <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments.
47 72
48 73
49 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_LabeledEval.html</help> 74 For more information, visit http://www.openms.de/documentation/UTILS_LabeledEval.html]]></help>
75 <expand macro="references"/>
50 </tool> 76 </tool>