Mercurial > repos > galaxyp > openms_xmlvalidator
comparison XMLValidator.xml @ 9:dba6eb59efc8 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 27 Aug 2020 19:45:01 -0400 |
parents | 68c2fe7ee7d4 |
children | 75bb0f81cfa3 |
comparison
equal
deleted
inserted
replaced
8:ffbc36a9ec0d | 9:dba6eb59efc8 |
---|---|
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="XMLValidator" name="XMLValidator" version="2.3.0"> | 4 <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Validates XML files against an XSD schema.</description> | 5 <description>Validates XML files against an XSD schema.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">XMLValidator</token> | 7 <token name="@EXECUTABLE@">XMLValidator</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[XMLValidator | 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 #if $schema: | |
22 mkdir schema && | |
23 ln -s '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' && | |
17 #end if | 24 #end if |
18 #if $param_schema: | 25 |
19 -schema $param_schema | 26 ## Main program call |
27 | |
28 set -o pipefail && | |
29 @EXECUTABLE@ -write_ctd ./ && | |
30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
32 -in | |
33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
34 #if $schema: | |
35 -schema | |
36 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' | |
20 #end if | 37 #end if |
21 #if $adv_opts.adv_opts_selector=='advanced': | 38 | tee '$stdout' |
22 #if $adv_opts.param_force: | 39 |
23 -force | 40 ## Postprocessing |
24 #end if | 41 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
25 #end if | 42 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
26 > $param_stdout | 43 #end if]]></command> |
27 ]]></command> | 44 <configfiles> |
45 <inputs name="args_json" data_style="paths"/> | |
46 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
47 </configfiles> | |
28 <inputs> | 48 <inputs> |
29 <param name="param_in" type="data" format="mzml,mzData,featurexml,mzid,idxml,consensusxml,mzxml,txt,pepxml,traml,xml" optional="False" label="file to validate" help="(-in) "/> | 49 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" optional="false" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/> |
30 <param name="param_schema" type="data" format="txt" optional="True" label="schema to validate against" help="(-schema) <br>If no schema is given, the file is validated against the latest schema of the file type"/> | 50 <param name="schema" argument="-schema" type="data" format="xml" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xml data sets(s)"/> |
31 <expand macro="advanced_options"> | 51 <expand macro="adv_opts_macro"> |
32 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 52 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
53 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
54 <expand macro="list_string_san"/> | |
55 </param> | |
33 </expand> | 56 </expand> |
57 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
59 </param> | |
34 </inputs> | 60 </inputs> |
35 <outputs> | 61 <outputs> |
36 <data name="param_stdout" format="txt" label="Output from stdout"/> | 62 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> |
63 <filter>OPTIONAL_OUTPUTS is None</filter> | |
64 </data> | |
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
67 </data> | |
37 </outputs> | 68 </outputs> |
38 <help>Validates XML files against an XSD schema. | 69 <tests> |
70 <expand macro="autotest_XMLValidator"/> | |
71 <expand macro="manutest_XMLValidator"/> | |
72 </tests> | |
73 <help><![CDATA[Validates XML files against an XSD schema. | |
39 | 74 |
40 | 75 |
41 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_XMLValidator.html</help> | 76 For more information, visit http://www.openms.de/documentation/UTILS_XMLValidator.html]]></help> |
77 <expand macro="references"/> | |
42 </tool> | 78 </tool> |