Mercurial > repos > galaxyp > openms_cvinspector
comparison CVInspector.xml @ 17:f95704542c63 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 18:56:45 +0000 |
parents | 53695d887eaa |
children | c8e5389abfc5 |
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16:7363ca9e41bd | 17:f95704542c63 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 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.--> | 2 <!--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]--> | 3 <!--Proposed Tool Section: [Utilities]--> |
4 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <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> | 5 <description>A tool for visualization and validation of PSI mapping and CV files.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">CVInspector</token> | 7 <token name="@EXECUTABLE@">CVInspector</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
16 #import re | 14 #import re |
17 | 15 |
18 ## Preprocessing | 16 ## Preprocessing |
19 mkdir cv_files && | 17 mkdir cv_files_cond.cv_files && |
20 ${ ' '.join(["ln -s '%s' 'cv_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _]) } | 18 #if $cv_files_cond.cv_files_select == "no" |
21 #if $mapping_file: | 19 mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && |
22 mkdir mapping_file && | 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])} |
23 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && | 21 #else |
22 ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' && | |
24 #end if | 23 #end if |
24 mkdir mapping_file && | |
25 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && | |
25 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 26 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
26 mkdir html && | 27 mkdir html && |
27 #end if | 28 #end if |
28 | 29 |
29 ## Main program call | 30 ## Main program call |
31 set -o pipefail && | 32 set -o pipefail && |
32 @EXECUTABLE@ -write_ctd ./ && | 33 @EXECUTABLE@ -write_ctd ./ && |
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | 34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
35 -cv_files | 36 -cv_files |
36 ${' '.join(["'cv_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])} | 37 #if $cv_files_cond.cv_files_select == "no" |
37 #if $mapping_file: | 38 ${' '.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])} |
38 -mapping_file | 39 #else |
39 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' | 40 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' |
40 #end if | 41 #end if |
42 -mapping_file | |
43 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' | |
41 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 44 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
42 -html | 45 -html |
43 'html/output.${gxy2omsext("html")}' | 46 'html/output.${gxy2omsext("html")}' |
44 #end if | 47 #end if |
45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | 48 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
56 <configfiles> | 59 <configfiles> |
57 <inputs name="args_json" data_style="paths"/> | 60 <inputs name="args_json" data_style="paths"/> |
58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 61 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
59 </configfiles> | 62 </configfiles> |
60 <inputs> | 63 <inputs> |
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)"/> | 64 <conditional name="cv_files_cond"> |
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)"> | 65 <param name="cv_files_select" type="select" label="Run tool in batch mode for -cv_files"> |
63 <expand macro="list_string_val"/> | 66 <option value="no">No: process all datasets jointly</option> |
64 <expand macro="list_string_san"/> | 67 <option value="yes">Yes: process each dataset in an independent job</option> |
68 </param> | |
69 <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)"/> | |
71 </when> | |
72 <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)"/> | |
74 </when> | |
75 </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)"> | |
77 <expand macro="list_string_val" name="cv_names"/> | |
78 <expand macro="list_string_san" name="cv_names"/> | |
65 </param> | 79 </param> |
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)"/> | 80 <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/> |
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)"> | 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)"> |
68 <expand macro="list_string_val"/> | 82 <expand macro="list_string_val" name="ignore_cv"/> |
69 <expand macro="list_string_san"/> | 83 <expand macro="list_string_san" name="ignore_cv"/> |
70 </param> | 84 </param> |
71 <expand macro="adv_opts_macro"> | 85 <expand macro="adv_opts_macro"> |
72 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 86 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
73 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 87 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
74 <expand macro="list_string_san"/> | 88 <expand macro="list_string_san" name="test"/> |
75 </param> | 89 </param> |
76 </expand> | 90 </expand> |
77 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
78 <option value="html_FLAG">html (Writes an HTML version of the mapping file with annotated CV terms)</option> | 92 <option value="html_FLAG">html (Writes an HTML version of the mapping file with annotated CV terms)</option> |
79 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
88 </data> | 102 </data> |
89 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
90 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
91 </data> | 105 </data> |
92 </outputs> | 106 </outputs> |
93 <tests> | 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 --> |
94 <expand macro="autotest_CVInspector"/> | 108 <test expect_num_outputs="1"> |
95 <expand macro="manutest_CVInspector"/> | 109 <param name="adv_opts|test" value="true"/> |
96 </tests> | 110 <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> |
111 <param name="cv_names" value="XLMOD"/> | |
112 <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> | |
113 <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> | |
114 <output name="html" ftype="html" value="CVInspector.html"/> | |
115 </test> | |
116 </tests> | |
97 <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. |
98 | 118 |
99 | 119 |
100 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_CVInspector.html]]></help> | 120 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_CVInspector.html]]></help> |
101 <expand macro="references"/> | 121 <expand macro="references"/> |
102 </tool> | 122 </tool> |