Mercurial > repos > galaxyp > openms_idscoreswitcher

annotate IDScoreSwitcher.xml @ 14:5a56ed4fb4c2 draft default tip

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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 21:29:53 +0000
parents 4204882495f2
children
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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: [Identification Processing]-->
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3 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Switches between different scores of peptide or protein hits in identification data</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">IDScoreSwitcher</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 in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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21
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 -out
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29 'out/output.${gxy2omsext("idxml")}'
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31 ## Postprocessing
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32 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <param argument="-in" type="data" format="idxml" label="Input file" help=" select idxml data sets(s)"/>
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42 <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
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43 <expand macro="list_string_san" name="new_score"/>
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44 </param>
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45 <param argument="-new_score_orientation" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help="">
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46 <option value="lower_better">lower_better</option>
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47 <option value="higher_better">higher_better</option>
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48 <expand macro="list_string_san" name="new_score_orientation"/>
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49 </param>
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50 <param argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
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51 <expand macro="list_string_san" name="new_score_type"/>
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52 </param>
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53 <param argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
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54 <expand macro="list_string_san" name="old_score"/>
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55 </param>
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56 <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
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57 <expand macro="adv_opts_macro">
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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="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <!-- TOPP_IDScoreSwitcher_1 -->
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75 <test expect_num_outputs="2">
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76 <section name="adv_opts">
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77 <param name="force" value="false"/>
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78 <param name="test" value="true"/>
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79 </section>
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80 <param name="in" value="IDFileConverter_12_output.idXML"/>
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81 <output name="out" value="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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82 <param name="new_score" value="Percolator_PEP"/>
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83 <param name="new_score_orientation" value="lower_better"/>
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84 <param name="new_score_type" value="Posterior Error Probability"/>
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85 <param name="old_score" value="Percolator_qvalue"/>
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86 <param name="proteins" value="false"/>
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87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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88 <output name="ctd_out" ftype="xml">
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89 <assert_contents>
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90 <is_valid_xml/>
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91 </assert_contents>
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92 </output>
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93 <assert_stdout>
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94 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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95 </assert_stdout>
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96 </test>
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97 <!-- TOPP_IDScoreSwitcher_2 -->
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98 <test expect_num_outputs="2">
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99 <section name="adv_opts">
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100 <param name="force" value="false"/>
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101 <param name="test" value="true"/>
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102 </section>
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103 <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
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104 <output name="out" value="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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105 <param name="new_score" value="Posterior Probability_score"/>
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106 <param name="new_score_orientation" value="higher_better"/>
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107 <param name="new_score_type" value="Posterior Probability"/>
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108 <param name="old_score" value=""/>
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109 <param name="proteins" value="true"/>
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110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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111 <output name="ctd_out" ftype="xml">
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112 <assert_contents>
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113 <is_valid_xml/>
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114 </assert_contents>
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115 </output>
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116 <assert_stdout>
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117 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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118 </assert_stdout>
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119 </test>
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120 </tests>
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121 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data
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122
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123
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124 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDScoreSwitcher.html]]></help>
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125 <expand macro="references"/>
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126 </tool>