Mercurial > repos > galaxyp > openms_cvinspector

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 19:14:49 +0000
parents a797d29f3356
children
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--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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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>A tool for visualization and validation of PSI mapping and CV files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">CVInspector</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir cv_files &&
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20 ${ ' '.join(["ln -s '%s' 'cv_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _]) }
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21 #if $mapping_file:
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22 mkdir mapping_file &&
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23 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
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24 #end if
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25 #if "html_FLAG" in str($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 ${' '.join(["'cv_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])}
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37 #if $mapping_file:
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38 -mapping_file
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39 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
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40 #end if
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41 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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42 -html
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43 'html/output.${gxy2omsext("html")}'
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44 #end if
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45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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46 | tee '$stdout'
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47 #end if
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48
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49 ## Postprocessing
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50 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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51 && mv 'html/output.${gxy2omsext("html")}' '$html'
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52 #end if
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53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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55 #end if]]></command>
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56 <configfiles>
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57 <inputs name="args_json" data_style="paths"/>
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58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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59 </configfiles>
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60 <inputs>
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61 <param name="cv_files" argument="-cv_files" type="data" format="obo" multiple="true" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
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62 <param name="cv_names" argument="-cv_names" type="text" optional="false" 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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63 <expand macro="list_string_val"/>
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64 <expand macro="list_string_san"/>
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65 </param>
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66 <param name="mapping_file" argument="-mapping_file" type="data" format="xml" optional="true" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
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67 <param name="ignore_cv" argument="-ignore_cv" type="text" optional="true" 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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68 <expand macro="list_string_val"/>
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69 <expand macro="list_string_san"/>
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70 </param>
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71 <expand macro="adv_opts_macro">
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72 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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73 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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74 <expand macro="list_string_san"/>
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75 </param>
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76 </expand>
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77 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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78 <option value="html_FLAG">html (Writes an HTML version of the mapping file with annotated CV terms)</option>
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79 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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80 </param>
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81 </inputs>
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82 <outputs>
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83 <data name="html" label="${tool.name} on ${on_string}: html" format="html">
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84 <filter>OPTIONAL_OUTPUTS is not None and "html_FLAG" in OPTIONAL_OUTPUTS</filter>
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85 </data>
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86 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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87 <filter>OPTIONAL_OUTPUTS is None</filter>
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88 </data>
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89 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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90 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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91 </data>
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92 </outputs>
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93 <tests>
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94 <expand macro="autotest_CVInspector"/>
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95 <expand macro="manutest_CVInspector"/>
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96 </tests>
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97 <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files.
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98
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99
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100 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_CVInspector.html]]></help>
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101 <expand macro="references"/>
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102 </tool>