Mercurial > repos > galaxyp > openms_semanticvalidator
comparison SemanticValidator.xml @ 9:702ed84d9f4c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:18:18 +0000 |
parents | 6f22beeb9f32 |
children | b60c5420dac6 |
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8:a17482bfebe5 | 9:702ed84d9f4c |
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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="SemanticValidator" name="SemanticValidator" version="2.3.0"> | 4 <tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>SemanticValidator for semantically validating certain XML files.</description> | 5 <description>SemanticValidator for semantically validating certain XML files.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">SemanticValidator</token> | 7 <token name="@EXECUTABLE@">SemanticValidator</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[SemanticValidator | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | |
21 mkdir mapping_file && | |
22 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && | |
23 #if $cv: | |
24 mkdir cv && | |
25 ${ ' '.join(["ln -s '%s' 'cv/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _]) } | |
17 #end if | 26 #end if |
18 #if $param_mapping_file: | 27 |
19 -mapping_file $param_mapping_file | 28 ## Main program call |
29 | |
30 set -o pipefail && | |
31 @EXECUTABLE@ -write_ctd ./ && | |
32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
34 -in | |
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
36 -mapping_file | |
37 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' | |
38 #if $cv: | |
39 -cv | |
40 ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])} | |
20 #end if | 41 #end if |
21 -cv | 42 | tee '$stdout' |
22 #for token in $param_cv: | 43 |
23 $token | 44 ## Postprocessing |
24 #end for | 45 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
25 #if $adv_opts.adv_opts_selector=='advanced': | 46 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
26 #if $adv_opts.param_force: | 47 #end if]]></command> |
27 -force | 48 <configfiles> |
28 #end if | 49 <inputs name="args_json" data_style="paths"/> |
29 #end if | 50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
30 > $param_stdout | 51 </configfiles> |
31 ]]></command> | |
32 <inputs> | 52 <inputs> |
33 <param name="param_in" type="data" format="analysisXML,mzml,traml,mzid,mzData,xml" optional="False" label="Input file (any xml file)" help="(-in) "/> | 53 <param name="in" argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" optional="false" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/> |
34 <param name="param_mapping_file" type="data" format="xml" optional="False" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help="(-mapping_file) "/> | 54 <param name="mapping_file" argument="-mapping_file" type="data" format="xml" optional="false" 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)"/> |
35 <param name="param_cv" type="data" format="obo" multiple="true" optional="True" size="30" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help="(-cv) "> | 55 <param name="cv" 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)"/> |
36 <sanitizer> | 56 <expand macro="adv_opts_macro"> |
37 <valid initial="string.printable"> | 57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
38 <remove value="'"/> | 58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
39 <remove value="""/> | 59 <expand macro="list_string_san"/> |
40 </valid> | 60 </param> |
41 </sanitizer> | 61 </expand> |
62 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
42 </param> | 64 </param> |
43 <expand macro="advanced_options"> | |
44 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
45 </expand> | |
46 </inputs> | 65 </inputs> |
47 <outputs> | 66 <outputs> |
48 <data name="param_stdout" format="txt" label="Output from stdout"/> | 67 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> |
68 <filter>OPTIONAL_OUTPUTS is None</filter> | |
69 </data> | |
70 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
71 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
72 </data> | |
49 </outputs> | 73 </outputs> |
50 <help>SemanticValidator for semantically validating certain XML files. | 74 <tests> |
75 <expand macro="autotest_SemanticValidator"/> | |
76 <expand macro="manutest_SemanticValidator"/> | |
77 </tests> | |
78 <help><![CDATA[SemanticValidator for semantically validating certain XML files. | |
51 | 79 |
52 | 80 |
53 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SemanticValidator.html</help> | 81 For more information, visit http://www.openms.de/documentation/UTILS_SemanticValidator.html]]></help> |
82 <expand macro="references"/> | |
54 </tool> | 83 </tool> |