Mercurial > repos > galaxyp > openms_ffeval

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:01 +0000
parents a02af506fe40
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44d9229ac23d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="FFEval" name="FFEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Evaluation tool for feature detection algorithms.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FFEval</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($in.ext)' &&
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19 mkdir truth &&
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20 ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
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21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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22 mkdir out &&
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23 #end if
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24 #if $abort_reasons:
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25 mkdir abort_reasons &&
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26 ln -s '$abort_reasons' 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)' &&
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27 #end if
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28 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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29 mkdir out_roc &&
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30 #end if
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32 ## Main program call
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34 set -o pipefail &&
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35 @EXECUTABLE@ -write_ctd ./ &&
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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38 -in
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39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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40 -truth
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41 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
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42 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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43 -out
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44 'out/output.${gxy2omsext("featurexml")}'
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45 #end if
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46 #if $abort_reasons:
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47 -abort_reasons
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48 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)'
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49 #end if
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50 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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51 -out_roc
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52 'out_roc/output.${gxy2omsext("csv")}'
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53 #end if
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54 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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55 | tee '$stdout'
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56 #end if
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58 ## Postprocessing
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59 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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60 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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61 #end if
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62 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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63 && mv 'out_roc/output.${gxy2omsext("csv")}' '$out_roc'
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64 #end if
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65 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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66 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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67 #end if]]></command>
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68 <configfiles>
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69 <inputs name="args_json" data_style="paths"/>
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70 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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71 </configfiles>
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72 <inputs>
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73 <param argument="-in" type="data" format="featurexml" optional="false" label="Feature input file, which contains the data to be tested against the truth file" help=" select featurexml data sets(s)"/>
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74 <param argument="-truth" type="data" format="featurexml" optional="false" label="Truth feature file that defines what features should be found" help=" select featurexml data sets(s)"/>
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75 <param argument="-rt_tol" type="float" optional="true" min="0.0" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help=""/>
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76 <param argument="-rt_tol_abs" type="float" optional="true" min="-1.0" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help=""/>
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77 <param argument="-mz_tol" type="float" optional="true" min="0.0" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help=""/>
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78 <param argument="-abort_reasons" type="data" format="featurexml" optional="true" label="Feature file containing seeds with abort reasons" help=" select featurexml data sets(s)"/>
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79 <expand macro="adv_opts_macro">
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80 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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81 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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82 <expand macro="list_string_san" name="test"/>
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83 </param>
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84 </expand>
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85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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86 <option value="out_FLAG">out (Feature output file)</option>
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87 <option value="out_roc_FLAG">out_roc (If given, a ROC curve file is created (ROC points based on intensity threshold))</option>
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88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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89 </param>
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90 </inputs>
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91 <outputs>
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92 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
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93 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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94 </data>
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95 <data name="out_roc" label="${tool.name} on ${on_string}: out_roc" format="csv">
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96 <filter>OPTIONAL_OUTPUTS is not None and "out_roc_FLAG" in OPTIONAL_OUTPUTS</filter>
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97 </data>
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98 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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99 <filter>OPTIONAL_OUTPUTS is None</filter>
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100 </data>
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101 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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102 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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103 </data>
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104 </outputs>
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105 <tests><test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
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106 <param name="adv_opts|test" value="true"/>
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107 <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
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108 <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
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109 <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
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110 <output name="out" value="FFEval.featureXML" compare="sim_size"/>
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111 <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
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112 </test>
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113 </tests>
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114 <help><![CDATA[Evaluation tool for feature detection algorithms.
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115
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116
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117 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FFEval.html]]></help>
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118 <expand macro="references"/>
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119 </tool>