Mercurial > repos > galaxyp > openms_ffeval

annotate FFEval.xml @ 15:afcacccf0683 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:00:51 +0000
parents 85a73e92abae
children
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e3e4800c7bb6 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@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir truth &&
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22 ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
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23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir out &&
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25 #end if
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26 #if $abort_reasons:
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27 mkdir abort_reasons &&
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28 ln -s '$abort_reasons' 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)' &&
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29 #end if
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30 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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31 mkdir out_roc &&
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32 #end if
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34 ## Main program call
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85a73e92abae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 set -o pipefail &&
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37 @EXECUTABLE@ -write_ctd ./ &&
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38 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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39 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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40 -in
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41 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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42 -truth
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43 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
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44 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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45 -out
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46 'out/output.${gxy2omsext("featurexml")}'
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47 #end if
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48 #if $abort_reasons:
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49 -abort_reasons
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50 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)'
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51 #end if
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52 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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53 -out_roc
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54 'out_roc/output.${gxy2omsext("csv")}'
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55 #end if
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56 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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57 | tee '$stdout'
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58 #end if
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59
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60 ## Postprocessing
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61 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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62 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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63 #end if
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64 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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65 && mv 'out_roc/output.${gxy2omsext("csv")}' '$out_roc'
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66 #end if
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67 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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68 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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69 #end if]]></command>
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70 <configfiles>
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71 <inputs name="args_json" data_style="paths"/>
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72 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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73 </configfiles>
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74 <inputs>
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75 <param name="in" 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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76 <param name="truth" 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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77 <param name="rt_tol" 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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78 <param name="rt_tol_abs" 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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79 <param name="mz_tol" 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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80 <param name="abort_reasons" 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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81 <expand macro="adv_opts_macro">
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82 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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83 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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84 <expand macro="list_string_san"/>
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85 </param>
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86 </expand>
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87 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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88 <option value="out_FLAG">out (Feature output file)</option>
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89 <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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90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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91 </param>
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92 </inputs>
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93 <outputs>
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94 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
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95 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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96 </data>
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97 <data name="out_roc" label="${tool.name} on ${on_string}: out_roc" format="csv">
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98 <filter>OPTIONAL_OUTPUTS is not None and "out_roc_FLAG" in OPTIONAL_OUTPUTS</filter>
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99 </data>
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100 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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101 <filter>OPTIONAL_OUTPUTS is None</filter>
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102 </data>
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103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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105 </data>
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106 </outputs>
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107 <tests>
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108 <expand macro="autotest_FFEval"/>
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109 <expand macro="manutest_FFEval"/>
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110 </tests>
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111 <help><![CDATA[Evaluation tool for feature detection algorithms.
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112
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113
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114 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FFEval.html]]></help>
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115 <expand macro="references"/>
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116 </tool>