Mercurial > repos > galaxyp > openms_cvinspector
comparison CVInspector.xml @ 13:3b585b370ab8 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 20:14:44 +0000 |
parents | 8a11c915c25b |
children | 53695d887eaa |
comparison
equal
deleted
inserted
replaced
12:29dbef61b882 | 13:3b585b370ab8 |
---|---|
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="2.3.0"> | 4 <tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
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> | |
9 </macros> | 11 </macros> |
10 <expand macro="references"/> | 12 <expand macro="requirements"/> |
11 <expand macro="stdio"/> | 13 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
13 <command detect_errors="aggressive"><![CDATA[CVInspector | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 -cv_files | 18 ## Preprocessing |
16 #for token in $param_cv_files: | 19 mkdir cv_files && |
17 $token | 20 ${ ' '.join(["ln -s '%s' 'cv_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _]) } |
18 #end for | 21 #if $mapping_file: |
19 | 22 mkdir mapping_file && |
20 #if $rep_param_cv_names: | 23 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && |
21 -cv_names | |
22 #for token in $rep_param_cv_names: | |
23 #if " " in str(token): | |
24 "$token.param_cv_names" | |
25 #else | |
26 $token.param_cv_names | |
27 #end if | |
28 #end for | |
29 #end if | 24 #end if |
30 #if $param_mapping_file: | 25 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
31 -mapping_file $param_mapping_file | 26 mkdir html && |
32 #end if | 27 #end if |
33 | 28 |
34 #if $rep_param_ignore_cv: | 29 ## Main program call |
35 -ignore_cv | 30 |
36 #for token in $rep_param_ignore_cv: | 31 set -o pipefail && |
37 #if " " in str(token): | 32 @EXECUTABLE@ -write_ctd ./ && |
38 "$token.param_ignore_cv" | 33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
39 #else | 34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
40 $token.param_ignore_cv | 35 -cv_files |
41 #end if | 36 ${' '.join(["'cv_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])} |
42 #end for | 37 #if $mapping_file: |
38 -mapping_file | |
39 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' | |
43 #end if | 40 #end if |
44 #if $param_html: | 41 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
45 -html $param_html | 42 -html |
43 'html/output.${gxy2omsext("html")}' | |
46 #end if | 44 #end if |
47 #if $adv_opts.adv_opts_selector=='advanced': | 45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
48 #if $adv_opts.param_force: | 46 | tee '$stdout' |
49 -force | |
50 #end if | 47 #end if |
48 | |
49 ## Postprocessing | |
50 #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
51 && mv 'html/output.${gxy2omsext("html")}' '$html' | |
51 #end if | 52 #end if |
52 ]]></command> | 53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
54 && mv '@EXECUTABLE@.ctd' '$ctd_out' | |
55 #end if]]></command> | |
56 <configfiles> | |
57 <inputs name="args_json" data_style="paths"/> | |
58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
59 </configfiles> | |
53 <inputs> | 60 <inputs> |
54 <param name="param_cv_files" type="data" format="obo" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) "> | 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)"/> |
55 <sanitizer> | 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)"> |
56 <valid initial="string.printable"> | 63 <expand macro="list_string_val"/> |
57 <remove value="'"/> | 64 <expand macro="list_string_san"/> |
58 <remove value="""/> | |
59 </valid> | |
60 </sanitizer> | |
61 </param> | 65 </param> |
62 <repeat name="rep_param_cv_names" min="1" title="param_cv_names"> | 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)"/> |
63 <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) "> | 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)"> |
64 <sanitizer> | 68 <expand macro="list_string_val"/> |
65 <valid initial="string.printable"> | 69 <expand macro="list_string_san"/> |
66 <remove value="'"/> | 70 </param> |
67 <remove value="""/> | 71 <expand macro="adv_opts_macro"> |
68 </valid> | 72 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
69 </sanitizer> | 73 <param name="test" 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"/> | |
70 </param> | 75 </param> |
71 </repeat> | |
72 <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/> | |
73 <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv"> | |
74 <param name="param_ignore_cv" type="text" size="30" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help="(-ignore_cv) "> | |
75 <sanitizer> | |
76 <valid initial="string.printable"> | |
77 <remove value="'"/> | |
78 <remove value="""/> | |
79 </valid> | |
80 </sanitizer> | |
81 </param> | |
82 </repeat> | |
83 <expand macro="advanced_options"> | |
84 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
85 </expand> | 76 </expand> |
77 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> | |
78 <option value="html_FLAG">html (Enables the test mode (needed for internal use only))</option> | |
79 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
80 </param> | |
86 </inputs> | 81 </inputs> |
87 <outputs> | 82 <outputs> |
88 <data name="param_html" format="html"/> | 83 <data name="html" label="${tool.name} on ${on_string}: html" format="html"> |
84 <filter>OPTIONAL_OUTPUTS is not None and "html_FLAG" in OPTIONAL_OUTPUTS</filter> | |
85 </data> | |
86 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> | |
87 <filter>OPTIONAL_OUTPUTS is None</filter> | |
88 </data> | |
89 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
90 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
91 </data> | |
89 </outputs> | 92 </outputs> |
90 <help>A tool for visualization and validation of PSI mapping and CV files. | 93 <tests> |
94 <expand macro="autotest_CVInspector"/> | |
95 <expand macro="manutest_CVInspector"/> | |
96 </tests> | |
97 <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files. | |
91 | 98 |
92 | 99 |
93 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_CVInspector.html</help> | 100 For more information, visit http://www.openms.de/documentation/UTILS_CVInspector.html]]></help> |
101 <expand macro="references"/> | |
94 </tool> | 102 </tool> |