Mercurial > repos > galaxyp > openms_transformationevaluation

comparison TransformationEvaluation.xml @ 9:fc8e5a66639c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:03:59 +0000
parents b13820d2822f
children 24d0298006e1
comparison
equal deleted inserted replaced
8:4f9b7496fd54 9:fc8e5a66639c
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="TransformationEvaluation" name="TransformationEvaluation" version="2.3.0"> 4 <tool id="TransformationEvaluation" name="TransformationEvaluation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Applies a transformation to a range of values</description> 5 <description>Applies a transformation to a range of values</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">TransformationEvaluation</token> 7 <token name="@EXECUTABLE@">TransformationEvaluation</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[TransformationEvaluation 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($in.ext)' &&
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out &&
17 #end if 23 #end if
18 #if $param_out: 24
19 -out $param_out 25 ## Main program call
26
27 set -o pipefail &&
28 @EXECUTABLE@ -write_ctd ./ &&
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -in
32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
33 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 -out
35 'out/output.${gxy2omsext("trafoxml")}'
20 #end if 36 #end if
21 #if $param_min: 37 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
22 -min $param_min 38 | tee '$stdout'
23 #end if 39 #end if
24 #if $param_max: 40
25 -max $param_max 41 ## Postprocessing
42 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
43 && mv 'out/output.${gxy2omsext("trafoxml")}' '$out'
26 #end if 44 #end if
27 #if $param_step: 45 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
28 -step $param_step 46 && mv '@EXECUTABLE@.ctd' '$ctd_out'
29 #end if 47 #end if]]></command>
30 #if $adv_opts.adv_opts_selector=='advanced': 48 <configfiles>
31 #if $adv_opts.param_force: 49 <inputs name="args_json" data_style="paths"/>
32 -force 50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
33 #end if 51 </configfiles>
34 #end if
35 ]]></command>
36 <inputs> 52 <inputs>
37 <param name="param_in" type="data" format="trafoxml" optional="False" label="Input file containing the transformation description" help="(-in) "/> 53 <param name="in" argument="-in" type="data" format="trafoxml" optional="false" label="Input file containing the transformation description" help=" select trafoxml data sets(s)"/>
38 <param name="param_min" type="float" value="0.0" label="Minimum value to transform" help="(-min) "/> 54 <param name="min" argument="-min" type="float" optional="true" value="0.0" label="Minimum value to transform" help=""/>
39 <param name="param_max" type="float" value="0.0" label="Maximum value to transform (if at or below 'min', select a suitable maximum based on the transformation description)" help="(-max) "/> 55 <param name="max" argument="-max" type="float" optional="true" value="0.0" label="Maximum value to transform (if at or below 'min', select a suitable maximum based on the transformation description)" help=""/>
40 <param name="param_step" type="float" min="0.001" optional="True" value="1.0" label="Step size between 'min' and 'max'" help="(-step) "/> 56 <param name="step" argument="-step" type="float" optional="true" min="0.001" value="1.0" label="Step size between 'min' and 'max'" help=""/>
41 <expand macro="advanced_options"> 57 <expand macro="adv_opts_macro">
42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 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="false">
64 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
66 </param>
44 </inputs> 67 </inputs>
45 <outputs> 68 <outputs>
46 <data name="param_out" format="trafoxml"/> 69 <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml">
70 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data>
72 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
73 <filter>OPTIONAL_OUTPUTS is None</filter>
74 </data>
75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
77 </data>
47 </outputs> 78 </outputs>
48 <help>Applies a transformation to a range of values 79 <tests>
80 <expand macro="autotest_TransformationEvaluation"/>
81 <expand macro="manutest_TransformationEvaluation"/>
82 </tests>
83 <help><![CDATA[Applies a transformation to a range of values
49 84
50 85
51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_TransformationEvaluation.html</help> 86 For more information, visit http://www.openms.de/documentation/UTILS_TransformationEvaluation.html]]></help>
87 <expand macro="references"/>
52 </tool> 88 </tool>