Mercurial > repos > galaxyp > openms_cvinspector

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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 21:28:01 +0000
parents f95704542c63
children
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e97a8b65aa3c 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="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>A tool for visualization and validation of PSI mapping and CV files</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">CVInspector</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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14
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15 ## Preprocessing
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16 mkdir cv_files_cond.cv_files &&
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17 #if $cv_files_cond.cv_files_select == "no"
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18 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} &&
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19 ${' '.join(["cp '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
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20 #else
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21 cp '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
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22 #end if
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23 mkdir mapping_file &&
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24 cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
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25 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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26 mkdir html &&
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27 #end if
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -cv_files
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36 #if $cv_files_cond.cv_files_select == "no"
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37 ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])}
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38 #else
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39 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)'
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40 #end if
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41 -mapping_file
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42 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
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43 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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44 -html
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45 'html/output.${gxy2omsext("html")}'
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46 #end if
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47 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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48 | tee '$stdout'
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49 #end if
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50
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51 ## Postprocessing
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52 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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53 && mv 'html/output.${gxy2omsext("html")}' '$html'
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54 #end if
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55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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57 #end if]]></command>
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58 <configfiles>
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59 <inputs name="args_json" data_style="paths"/>
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60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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61 </configfiles>
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62 <inputs>
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63 <conditional name="cv_files_cond">
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64 <param name="cv_files_select" type="select" label="Run tool in batch mode for -cv_files">
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65 <option value="no">No: process all datasets jointly</option>
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66 <option value="yes">Yes: process each dataset in an independent job</option>
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67 </param>
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68 <when value="no">
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69 <param argument="-cv_files" type="data" format="obo" multiple="true" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
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70 </when>
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71 <when value="yes">
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72 <param argument="-cv_files" type="data" format="obo" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
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73 </when>
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74 </conditional>
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75 <param argument="-cv_names" type="text" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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76 <expand macro="list_string_val" name="cv_names"/>
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77 <expand macro="list_string_san" name="cv_names"/>
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78 </param>
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79 <param argument="-mapping_file" type="data" format="xml" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
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80 <param argument="-ignore_cv" type="text" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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81 <expand macro="list_string_val" name="ignore_cv"/>
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82 <expand macro="list_string_san" name="ignore_cv"/>
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83 </param>
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84 <expand macro="adv_opts_macro">
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85 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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86 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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87 <expand macro="list_string_san" name="test"/>
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88 </param>
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89 </expand>
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90 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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91 <option value="html_FLAG">html (Writes an HTML version of the mapping file with annotated CV terms)</option>
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92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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93 </param>
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94 </inputs>
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95 <outputs>
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96 <data name="html" label="${tool.name} on ${on_string}: html" format="html">
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97 <filter>OPTIONAL_OUTPUTS is not None and "html_FLAG" in OPTIONAL_OUTPUTS</filter>
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98 </data>
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99 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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100 <filter>OPTIONAL_OUTPUTS is None</filter>
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101 </data>
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102 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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103 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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104 </data>
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105 </outputs>
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106 <tests>
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107 <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml -->
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108 <test expect_num_outputs="1">
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109 <param name="adv_opts|test" value="true"/>
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110 <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
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111 <param name="cv_names" value="XLMOD"/>
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112 <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
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113 <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
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114 <output name="html" ftype="html" value="CVInspector.html"/>
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115 </test>
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116 </tests>
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117 <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files.
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118
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119
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120 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CVInspector.html]]></help>
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121 <expand macro="references"/>
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122 </tool>