Mercurial > repos > galaxyp > openms_seedlistgenerator

annotate SeedListGenerator.xml @ 8:f6076d07a33a 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 21:39:33 +0000
parents f3c72f54b9eb
children
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c82757bc39d7 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: [Quantitation]-->
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3 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Generates seed lists for feature detection</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">SeedListGenerator</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($in.ext)' &&
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18 mkdir out_prefix &&
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20 ## Main program call
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__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_prefix
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29 out_prefix/
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31 ## Postprocessing
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32 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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33 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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34 #end if]]></command>
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35 <configfiles>
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36 <inputs name="args_json" data_style="paths"/>
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37 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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38 </configfiles>
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39 <inputs>
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40 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file (see below for details)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
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41 <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
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42 <expand macro="adv_opts_macro">
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43 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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44 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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45 <expand macro="list_string_san" name="test"/>
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46 </param>
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47 </expand>
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48 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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49 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <collection type="list" name="out_prefix" label="${tool.name} on ${on_string}: out_prefix">
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54 <discover_datasets directory="out_prefix" recurse="true" format="featurexml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
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55 </collection>
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56 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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57 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <!-- TOPP_SeedListGenerator_1 -->
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62 <!-- TOPP_SeedListGenerator_2 -->
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63 <!-- TOPP_SeedListGenerator_3 -->
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64 <test expect_num_outputs="2">
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65 <section name="adv_opts">
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66 <param name="test" value="true"/>
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67 </section>
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68 <param name="in" value="PepXMLFile_test.mzML"/>
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69 <output_collection name="out_prefix" count="1">
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70 <element name="0" file="SeedListGenerator_1_output_tmp_0.featureXML" ftype="featurexml"/>
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71 </output_collection>
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72 <param name="use_peptide_mass" value="false"/>
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73 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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74 <output name="ctd_out" ftype="xml">
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75 <assert_contents>
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76 <is_valid_xml/>
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77 </assert_contents>
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78 </output>
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79 </test>
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80 <test expect_num_outputs="2">
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81 <section name="adv_opts">
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82 <param name="test" value="true"/>
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83 </section>
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84 <param name="in" value="IDMapper_1_output.featureXML"/>
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85 <output_collection name="out_prefix" count="1">
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86 <element name="0" file="SeedListGenerator_2_output_tmp_0.featureXML" ftype="featurexml"/>
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87 </output_collection>
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88 <param name="use_peptide_mass" value="false"/>
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89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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90 <output name="ctd_out" ftype="xml">
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91 <assert_contents>
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92 <is_valid_xml/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <test expect_num_outputs="2">
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97 <section name="adv_opts">
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98 <param name="test" value="true"/>
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99 </section>
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100 <param name="in" value="ConsensusXMLFile_1.consensusXML"/>
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101 <output_collection name="out_prefix" count="2">
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102 <element name="0" file="SeedListGenerator_3_output_tmp_0.featureXML" ftype="featurexml"/>
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103 <element name="1" file="SeedListGenerator_3_output_tmp_1.featureXML" ftype="featurexml"/>
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104 </output_collection>
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105 <param name="use_peptide_mass" value="false"/>
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106 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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107 <output name="ctd_out" ftype="xml">
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108 <assert_contents>
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109 <is_valid_xml/>
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110 </assert_contents>
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111 </output>
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112 </test>
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113 </tests>
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114 <help><![CDATA[Generates seed lists for feature detection.
0
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115
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116
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117 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SeedListGenerator.html]]></help>
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118 <expand macro="references"/>
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119 </tool>