Mercurial > repos > galaxyp > openms_semanticvalidator
comparison SemanticValidator.xml @ 13:ff9d0d1c2c1c 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 18:57:56 +0000 |
parents | b60c5420dac6 |
children | a421b4ddf47c |
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12:4af4658187e3 | 13:ff9d0d1c2c1c |
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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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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> | |
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@ |
18 ## Preprocessing | 16 ## Preprocessing |
19 mkdir in && | 17 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | 18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
21 mkdir mapping_file && | 19 mkdir mapping_file && |
22 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && | 20 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && |
23 #if $cv: | 21 #if $cv_cond.cv: |
24 mkdir cv && | 22 mkdir cv_cond.cv && |
25 ${ ' '.join(["ln -s '%s' 'cv/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _]) } | 23 #if $cv_cond.cv_select == "no" |
24 mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} && | |
25 ${' '.join(["ln -s '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])} | |
26 #else | |
27 ln -s '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' && | |
28 #end if | |
26 #end if | 29 #end if |
27 | 30 |
28 ## Main program call | 31 ## Main program call |
29 | 32 |
30 set -o pipefail && | 33 set -o pipefail && |
33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
34 -in | 37 -in |
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | 38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
36 -mapping_file | 39 -mapping_file |
37 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' | 40 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' |
38 #if $cv: | 41 #if $cv_cond.cv: |
39 -cv | 42 -cv |
40 ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])} | 43 #if $cv_cond.cv_select == "no" |
44 ${' '.join(["'cv_cond.cv/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])} | |
45 #else | |
46 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' | |
47 #end if | |
41 #end if | 48 #end if |
42 | tee '$stdout' | 49 | tee '$stdout' |
43 | 50 |
44 ## Postprocessing | 51 ## Postprocessing |
45 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 52 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
48 <configfiles> | 55 <configfiles> |
49 <inputs name="args_json" data_style="paths"/> | 56 <inputs name="args_json" data_style="paths"/> |
50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
51 </configfiles> | 58 </configfiles> |
52 <inputs> | 59 <inputs> |
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)"/> | 60 <param 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)"/> |
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)"/> | 61 <param 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)"/> |
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)"/> | 62 <conditional name="cv_cond"> |
63 <param name="cv_select" type="select" label="Run tool in batch mode for -cv"> | |
64 <option value="no">No: process all datasets jointly</option> | |
65 <option value="yes">Yes: process each dataset in an independent job</option> | |
66 </param> | |
67 <when value="no"> | |
68 <param 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)"/> | |
69 </when> | |
70 <when value="yes"> | |
71 <param argument="-cv" type="data" format="obo" multiple="false" 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)"/> | |
72 </when> | |
73 </conditional> | |
56 <expand macro="adv_opts_macro"> | 74 <expand macro="adv_opts_macro"> |
57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 75 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 76 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
59 <expand macro="list_string_san"/> | 77 <expand macro="list_string_san" name="test"/> |
60 </param> | 78 </param> |
61 </expand> | 79 </expand> |
62 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 80 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 81 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
64 </param> | 82 </param> |
69 </data> | 87 </data> |
70 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 88 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
71 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 89 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
72 </data> | 90 </data> |
73 </outputs> | 91 </outputs> |
74 <tests> | 92 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> |
75 <expand macro="autotest_SemanticValidator"/> | 93 <param name="adv_opts|test" value="true"/> |
76 <expand macro="manutest_SemanticValidator"/> | 94 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> |
77 </tests> | 95 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> |
96 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> | |
97 <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> | |
98 </output> | |
99 </test> | |
100 </tests> | |
78 <help><![CDATA[SemanticValidator for semantically validating certain XML files. | 101 <help><![CDATA[SemanticValidator for semantically validating certain XML files. |
79 | 102 |
80 | 103 |
81 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SemanticValidator.html]]></help> | 104 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SemanticValidator.html]]></help> |
82 <expand macro="references"/> | 105 <expand macro="references"/> |
83 </tool> | 106 </tool> |