annotate TransformationEvaluation.xml @ 13:76ae6a5181b5 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:04:34 +0000
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="TransformationEvaluation" name="TransformationEvaluation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Applies a transformation to a range of values</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">TransformationEvaluation</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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20 mkdir out &&
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21 #end if
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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32 -out
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33 'out/output.${gxy2omsext("trafoxml")}'
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34 #end if
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35 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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36 | tee '$stdout'
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37 #end if
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38
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39 ## Postprocessing
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40 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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41 && mv 'out/output.${gxy2omsext("trafoxml")}' '$out'
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42 #end if
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43 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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44 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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45 #end if]]></command>
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46 <configfiles>
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47 <inputs name="args_json" data_style="paths"/>
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48 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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49 </configfiles>
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50 <inputs>
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51 <param argument="-in" type="data" format="trafoxml" optional="false" label="Input file containing the transformation description" help=" select trafoxml data sets(s)"/>
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52 <param argument="-min" type="float" optional="true" value="0.0" label="Minimum value to transform" help=""/>
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53 <param 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=""/>
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54 <param argument="-step" type="float" optional="true" min="0.001" value="1.0" label="Step size between 'min' and 'max'" help=""/>
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55 <expand macro="adv_opts_macro">
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56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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58 <expand macro="list_string_san" name="test"/>
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59 </param>
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60 </expand>
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61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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62 <option value="out_FLAG">out (Output file containing original and transformed values; if empty, output is written to the screen)</option>
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63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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64 </param>
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65 </inputs>
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66 <outputs>
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67 <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml">
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68 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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69 </data>
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70 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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71 <filter>OPTIONAL_OUTPUTS is None</filter>
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72 </data>
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73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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75 </data>
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76 </outputs>
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77 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
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78 <param name="adv_opts|test" value="true"/>
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79 <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
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80 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
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81 <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[Applies a transformation to a range of values
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85
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86
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87 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TransformationEvaluation.html]]></help>
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88 <expand macro="references"/>
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89 </tool>