Mercurial > repos > galaxyp > openms_openswathconfidencescoring

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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 21:43:51 +0000
parents c1809c05ae8c
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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: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Compute confidence scores for OpenSwath results</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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($in.ext)' &&
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18 mkdir lib &&
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19 cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
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20 mkdir out &&
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21 #if $trafo:
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22 mkdir trafo &&
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23 cp '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
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24 #end if
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26 ## Main program call
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28 set -o pipefail &&
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29 @EXECUTABLE@ -write_ctd ./ &&
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30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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32 -in
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33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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34 -lib
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35 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)'
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36 -out
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37 'out/output.${gxy2omsext("featurexml")}'
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38 #if $trafo:
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39 -trafo
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40 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)'
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41 #end if
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43 ## Postprocessing
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44 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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45 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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46 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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47 #end if]]></command>
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48 <configfiles>
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49 <inputs name="args_json" data_style="paths"/>
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50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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51 </configfiles>
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52 <inputs>
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53 <param argument="-in" type="data" format="featurexml" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
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54 <param argument="-lib" type="data" format="traml" label="Assay library" help=" select traml data sets(s)"/>
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55 <param argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
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56 <param argument="-decoys" type="integer" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
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57 <param argument="-transitions" type="integer" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
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58 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
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59 <param name="intercept" argument="-GLM:intercept" type="float" value="3.87333466" label="Intercept term" help=""/>
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60 <param name="delta_rt" argument="-GLM:delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
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61 <param name="dist_int" argument="-GLM:dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
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62 </section>
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63 <expand macro="adv_opts_macro">
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64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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65 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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66 <expand macro="list_string_san" name="test"/>
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67 </param>
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68 </expand>
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69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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70 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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71 </param>
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72 </inputs>
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73 <outputs>
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74 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <!-- TOPP_OpenSwathConfidenceScoring_1 -->
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81 <test expect_num_outputs="2">
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82 <section name="adv_opts">
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83 <param name="force" value="false"/>
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84 <param name="test" value="true"/>
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85 </section>
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86 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
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87 <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
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88 <output name="out" value="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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89 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
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90 <param name="decoys" value="1"/>
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91 <param name="transitions" value="2"/>
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92 <section name="GLM">
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93 <param name="intercept" value="3.87333466"/>
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94 <param name="delta_rt" value="-0.02898629"/>
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95 <param name="dist_int" value="-7.75880768"/>
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96 </section>
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97 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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98 <output name="ctd_out" ftype="xml">
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99 <assert_contents>
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100 <is_valid_xml/>
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101 </assert_contents>
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102 </output>
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103 <assert_stdout>
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104 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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105 </assert_stdout>
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106 </test>
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107 </tests>
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108 <help><![CDATA[Compute confidence scores for OpenSwath results
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109
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110
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111 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathConfidenceScoring.html]]></help>
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112 <expand macro="references"/>
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113 </tool>