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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:28:23 +0000
parents c940abd8d622
children
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cabf2360876a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--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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2 <!--Proposed Tool Section: [[for Developers]]-->
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3 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Compares two files, tolerating numeric differences</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">FuzzyDiff</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in1 &&
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17 cp '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
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18 mkdir in2 &&
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19 cp '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
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21 ## Main program call
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23 set -o pipefail &&
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24 @EXECUTABLE@ -write_ctd ./ &&
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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27 -in1
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28 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)'
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29 -in2
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30 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)'
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31 | tee '$stdout'
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32
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33 ## Postprocessing
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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36 #end if]]></command>
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37 <configfiles>
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38 <inputs name="args_json" data_style="paths"/>
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param argument="-in1" type="data" format="txt" label="first input file" help=" select txt data sets(s)"/>
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43 <param argument="-in2" type="data" format="txt" label="second input file" help=" select txt data sets(s)"/>
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44 <param argument="-ratio" type="float" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied. Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
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45 <param argument="-absdiff" type="float" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/>
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46 <param argument="-verbose" type="integer" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/>
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47 <param argument="-tab_width" type="integer" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
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48 <param argument="-first_column" type="integer" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
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49 <expand macro="adv_opts_macro">
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50 <param argument="-whitelist" type="text" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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51 <expand macro="list_string_val" name="whitelist"/>
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52 <expand macro="list_string_san" name="whitelist"/>
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53 </param>
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54 <param argument="-matched_whitelist" type="text" optional="true" value="" label="Lines where one file contains one string and the other file another string are skipped" help="Input is given as list of colon separated tuples, e.g. String1:String2 String3:String4 (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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55 <expand macro="list_string_val" name="matched_whitelist"/>
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56 <expand macro="list_string_san" name="matched_whitelist"/>
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57 </param>
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58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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59 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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60 <expand macro="list_string_san" name="test"/>
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61 </param>
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62 </expand>
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63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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69 <filter>OPTIONAL_OUTPUTS is None</filter>
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70 </data>
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71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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73 </data>
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74 </outputs>
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75 <tests>
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76 <!-- TOPP_FuzzyDiff_3 -->
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77 <test expect_num_outputs="1">
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78 <section name="adv_opts">
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79 <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
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80 <param name="force" value="false"/>
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81 <param name="test" value="true"/>
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82 </section>
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83 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
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84 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
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85 <param name="ratio" value="1.01"/>
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86 <param name="absdiff" value="0.01"/>
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87 <param name="verbose" value="1"/>
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88 <param name="tab_width" value="8"/>
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89 <param name="first_column" value="1"/>
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90 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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91 <output name="ctd_out" ftype="xml">
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92 <assert_contents>
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93 <is_valid_xml/>
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94 </assert_contents>
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95 </output>
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96 <assert_stdout>
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97 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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98 </assert_stdout>
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99 </test>
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100 </tests>
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101 <help><![CDATA[Compares two files, tolerating numeric differences.
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102
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103
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104 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FuzzyDiff.html]]></help>
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105 <expand macro="references"/>
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106 </tool>