Mercurial > repos > galaxyp > openms_semanticvalidator

annotate SemanticValidator.xml @ 11:b60c5420dac6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:21:06 +0000
parents 702ed84d9f4c
children ff9d0d1c2c1c
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>SemanticValidator for semantically validating certain XML files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SemanticValidator</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir mapping_file &&
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22 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
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23 #if $cv:
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24 mkdir cv &&
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25 ${ ' '.join(["ln -s '%s' 'cv/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _]) }
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26 #end if
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28 ## Main program call
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30 set -o pipefail &&
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31 @EXECUTABLE@ -write_ctd ./ &&
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32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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34 -in
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35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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36 -mapping_file
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37 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
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38 #if $cv:
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39 -cv
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40 ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])}
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41 #end if
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42 | tee '$stdout'
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44 ## Postprocessing
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45 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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46 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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47 #end if]]></command>
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48 <configfiles>
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49 <inputs name="args_json" data_style="paths"/>
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50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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51 </configfiles>
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52 <inputs>
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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)"/>
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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)"/>
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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)"/>
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56 <expand macro="adv_opts_macro">
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57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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59 <expand macro="list_string_san"/>
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60 </param>
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61 </expand>
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62 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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64 </param>
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65 </inputs>
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66 <outputs>
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67 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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68 <filter>OPTIONAL_OUTPUTS is None</filter>
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69 </data>
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70 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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71 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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72 </data>
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73 </outputs>
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74 <tests>
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75 <expand macro="autotest_SemanticValidator"/>
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76 <expand macro="manutest_SemanticValidator"/>
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77 </tests>
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78 <help><![CDATA[SemanticValidator for semantically validating certain XML files.
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f5dfeed76b4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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b60c5420dac6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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81 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SemanticValidator.html]]></help>
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702ed84d9f4c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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82 <expand macro="references"/>
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f5dfeed76b4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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83 </tool>