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comparison CVInspector.xml @ 18:c8e5389abfc5 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 21:28:01 +0000
parents f95704542c63
children
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17:f95704542c63 18:c8e5389abfc5
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 2 <!--Proposed Tool Section: [[for Developers]]-->
4 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>A tool for visualization and validation of PSI mapping and CV files.</description> 4 <description>A tool for visualization and validation of PSI mapping and CV files</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">CVInspector</token> 6 <token name="@EXECUTABLE@">CVInspector</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir cv_files_cond.cv_files && 16 mkdir cv_files_cond.cv_files &&
18 #if $cv_files_cond.cv_files_select == "no" 17 #if $cv_files_cond.cv_files_select == "no"
19 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && 18 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} &&
20 ${' '.join(["ln -s '%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])} 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])}
21 #else 20 #else
22 ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' && 21 cp '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' &&
23 #end if 22 #end if
24 mkdir mapping_file && 23 mkdir mapping_file &&
25 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && 24 cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
26 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 25 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
27 mkdir html && 26 mkdir html &&
28 #end if 27 #end if
29 28
30 ## Main program call 29 ## Main program call
65 <param name="cv_files_select" type="select" label="Run tool in batch mode for -cv_files"> 64 <param name="cv_files_select" type="select" label="Run tool in batch mode for -cv_files">
66 <option value="no">No: process all datasets jointly</option> 65 <option value="no">No: process all datasets jointly</option>
67 <option value="yes">Yes: process each dataset in an independent job</option> 66 <option value="yes">Yes: process each dataset in an independent job</option>
68 </param> 67 </param>
69 <when value="no"> 68 <when value="no">
70 <param 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)"/> 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)"/>
71 </when> 70 </when>
72 <when value="yes"> 71 <when value="yes">
73 <param argument="-cv_files" type="data" format="obo" multiple="false" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/> 72 <param argument="-cv_files" type="data" format="obo" label="List of ontology files in OBO format" help=" select obo data sets(s)"/>
74 </when> 73 </when>
75 </conditional> 74 </conditional>
76 <param 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)"> 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)">
77 <expand macro="list_string_val" name="cv_names"/> 76 <expand macro="list_string_val" name="cv_names"/>
78 <expand macro="list_string_san" name="cv_names"/> 77 <expand macro="list_string_san" name="cv_names"/>
79 </param> 78 </param>
80 <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/> 79 <param argument="-mapping_file" type="data" format="xml" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
81 <param 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)"> 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)">
82 <expand macro="list_string_val" name="ignore_cv"/> 81 <expand macro="list_string_val" name="ignore_cv"/>
83 <expand macro="list_string_san" name="ignore_cv"/> 82 <expand macro="list_string_san" name="ignore_cv"/>
84 </param> 83 </param>
85 <expand macro="adv_opts_macro"> 84 <expand macro="adv_opts_macro">
86 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 85 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
87 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 86 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
88 <expand macro="list_string_san" name="test"/> 87 <expand macro="list_string_san" name="test"/>
89 </param> 88 </param>
90 </expand> 89 </expand>
91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 90 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
92 <option value="html_FLAG">html (Writes an HTML version of the mapping file with annotated CV terms)</option> 91 <option value="html_FLAG">html (Writes an HTML version of the mapping file with annotated CV terms)</option>
102 </data> 101 </data>
103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 102 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 103 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
105 </data> 104 </data>
106 </outputs> 105 </outputs>
107 <tests><!-- 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 --> 106 <tests>
108 <test expect_num_outputs="1"> 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 -->
109 <param name="adv_opts|test" value="true"/> 108 <test expect_num_outputs="1">
110 <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> 109 <param name="adv_opts|test" value="true"/>
111 <param name="cv_names" value="XLMOD"/> 110 <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
112 <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> 111 <param name="cv_names" value="XLMOD"/>
113 <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> 112 <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
114 <output name="html" ftype="html" value="CVInspector.html"/> 113 <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
115 </test> 114 <output name="html" ftype="html" value="CVInspector.html"/>
116 </tests> 115 </test>
116 </tests>
117 <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files. 117 <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files.
118 118
119 119
120 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_CVInspector.html]]></help> 120 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_CVInspector.html]]></help>
121 <expand macro="references"/> 121 <expand macro="references"/>
122 </tool> 122 </tool>