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comparison SemanticValidator.xml @ 14:a421b4ddf47c draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:30:38 +0000
parents ff9d0d1c2c1c
children
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13:ff9d0d1c2c1c 14:a421b4ddf47c
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [[for Developers]]-->
4 <tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>SemanticValidator for semantically validating certain XML files.</description> 4 <description>SemanticValidator for semantically validating certain XML files</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SemanticValidator</token> 6 <token name="@EXECUTABLE@">SemanticValidator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir mapping_file && 18 mkdir mapping_file &&
20 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && 19 cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
21 #if $cv_cond.cv: 20 #if $cv_cond.cv:
22 mkdir cv_cond.cv && 21 mkdir cv_cond.cv &&
23 #if $cv_cond.cv_select == "no" 22 #if $cv_cond.cv_select == "no"
24 mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} && 23 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])} 24 ${' '.join(["cp '%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 25 #else
27 ln -s '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' && 26 cp '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' &&
28 #end if 27 #end if
29 #end if 28 #end if
30 29
31 ## Main program call 30 ## Main program call
32 31
55 <configfiles> 54 <configfiles>
56 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
58 </configfiles> 57 </configfiles>
59 <inputs> 58 <inputs>
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)"/> 59 <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,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)"/> 60 <param argument="-mapping_file" type="data" format="xml" 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)"/>
62 <conditional name="cv_cond"> 61 <conditional name="cv_cond">
63 <param name="cv_select" type="select" label="Run tool in batch mode for -cv"> 62 <param name="cv_select" type="select" label="Run tool in batch mode for -cv">
64 <option value="no">No: process all datasets jointly</option> 63 <option value="no">No: process all datasets jointly</option>
65 <option value="yes">Yes: process each dataset in an independent job</option> 64 <option value="yes">Yes: process each dataset in an independent job</option>
66 </param> 65 </param>
67 <when value="no"> 66 <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)"/> 67 <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> 68 </when>
70 <when value="yes"> 69 <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)"/> 70 <param argument="-cv" type="data" format="obo" 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> 71 </when>
73 </conditional> 72 </conditional>
74 <expand macro="adv_opts_macro"> 73 <expand macro="adv_opts_macro">
75 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 74 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
76 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 75 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
77 <expand macro="list_string_san" name="test"/> 76 <expand macro="list_string_san" name="test"/>
78 </param> 77 </param>
79 </expand> 78 </expand>
80 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 79 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
81 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </data> 86 </data>
88 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 87 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
89 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 88 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
90 </data> 89 </data>
91 </outputs> 90 </outputs>
92 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> 91 <tests>
93 <param name="adv_opts|test" value="true"/> 92 <test expect_num_outputs="1">
94 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> 93 <!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
95 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> 94 <param name="adv_opts|test" value="true"/>
96 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> 95 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
97 <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> 96 <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
98 </output> 97 <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
99 </test> 98 <assert_contents>
100 </tests> 99 <has_text text="Congratulations, the file is valid!"/>
100 </assert_contents>
101 </output>
102 </test>
103 </tests>
101 <help><![CDATA[SemanticValidator for semantically validating certain XML files. 104 <help><![CDATA[SemanticValidator for semantically validating certain XML files.
102 105
103 106
104 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SemanticValidator.html]]></help> 107 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SemanticValidator.html]]></help>
105 <expand macro="references"/> 108 <expand macro="references"/>
106 </tool> 109 </tool>