Mercurial > repos > galaxyp > openms_semanticvalidator

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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 21:30:38 +0000
parents ff9d0d1c2c1c
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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="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>SemanticValidator for semantically validating certain XML files</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">SemanticValidator</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($in.ext)' &&
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18 mkdir mapping_file &&
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19 cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
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20 #if $cv_cond.cv:
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21 mkdir cv_cond.cv &&
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22 #if $cv_cond.cv_select == "no"
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23 mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} &&
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24 ${' '.join(["cp '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])}
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25 #else
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26 cp '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' &&
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27 #end if
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28 #end if
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30 ## Main program call
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32 set -o pipefail &&
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33 @EXECUTABLE@ -write_ctd ./ &&
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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36 -in
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37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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38 -mapping_file
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39 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
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40 #if $cv_cond.cv:
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41 -cv
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42 #if $cv_cond.cv_select == "no"
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43 ${' '.join(["'cv_cond.cv/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])}
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44 #else
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45 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)'
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46 #end if
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47 #end if
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48 | tee '$stdout'
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50 ## Postprocessing
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51 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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52 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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53 #end if]]></command>
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54 <configfiles>
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55 <inputs name="args_json" data_style="paths"/>
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56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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57 </configfiles>
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58 <inputs>
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59 <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/>
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60 <param argument="-mapping_file" type="data" format="xml" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/>
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61 <conditional name="cv_cond">
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62 <param name="cv_select" type="select" label="Run tool in batch mode for -cv">
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63 <option value="no">No: process all datasets jointly</option>
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64 <option value="yes">Yes: process each dataset in an independent job</option>
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65 </param>
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66 <when value="no">
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67 <param argument="-cv" type="data" format="obo" multiple="true" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
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68 </when>
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69 <when value="yes">
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70 <param argument="-cv" type="data" format="obo" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/>
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71 </when>
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72 </conditional>
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73 <expand macro="adv_opts_macro">
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74 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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75 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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76 <expand macro="list_string_san" name="test"/>
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77 </param>
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78 </expand>
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79 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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81 </param>
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82 </inputs>
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83 <outputs>
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84 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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85 <filter>OPTIONAL_OUTPUTS is None</filter>
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86 </data>
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87 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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88 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <test expect_num_outputs="1">
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93 <!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
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94 <param name="adv_opts|test" value="true"/>
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95 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
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96 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
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97 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
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98 <assert_contents>
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99 <has_text text="Congratulations, the file is valid!"/>
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100 </assert_contents>
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101 </output>
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102 </test>
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103 </tests>
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104 <help><![CDATA[SemanticValidator for semantically validating certain XML files.
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105
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106
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107 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SemanticValidator.html]]></help>
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108 <expand macro="references"/>
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109 </tool>