Mercurial > repos > recetox > msmetaenhancer

annotate msmetaenhancer.xml @ 10:3e2cb0bc6959 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:30:31 +0000
parents 90745ecc5e9f
children 791bf4d9b06c
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1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy3">
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2 <description>annotate MS data</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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8 <xrefs>
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9 <xref type="bio.tools">msmetaenhancer</xref>
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10 </xrefs>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
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14 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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17 sh ${msmetaenhancer_python_cli}
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18 ]]> </command>
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20 <environment_variables>
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21 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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22 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
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23 </environment_variables>
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24
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25 <configfiles>
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26 <configfile name="msmetaenhancer_python_cli">
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27 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
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28 --input_file "$input_file" \
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29 --file_format "$input_file.ext" \
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30 --output_file "$output_file" \
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31 #if $options.logging.output_log == "TRUE":
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32 --log_file "$log_file" \
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33 --log_level "$options.logging.log_level" \
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34 #end if
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35 #if len($ordered_jobs) != 0:
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36 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
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37 #else:
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38 #set ordered_jobs = ""
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39 #end if
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40 #if $jobs != 'None':
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41 #set random_jobs = str($jobs)
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42 #else:
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43 #set random_jobs = ""
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44 #end if
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45 #set all_jobs = str($ordered_jobs) + str($random_jobs)
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46 --jobs "$all_jobs"
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47 </configfile>
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48 </configfiles>
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50 <inputs>
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51 <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tsv,xlsx" />
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53 <repeat name="ordered_jobs" title="Ordered conversions">
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54 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
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55 <expand macro="job_options" />
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56 </param>
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57 </repeat>
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59 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
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60 <expand macro="job_options" />
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61 </param>
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63 <section name="options" title="Options">
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64 <conditional name="logging">
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65 <param label="Save the log file" name="output_log" type="select" help="Preserve a log with details about the annotation process.">
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66 <option value="FALSE" selected="true">FALSE</option>
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67 <option value="TRUE">TRUE</option>
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68 </param>
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69 <when value="TRUE">
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70 <param name="log_level" type="select" label="Log level"
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71 help="Severity of log messages present in the log file.">
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72 <option value="error">ERROR</option>
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73 <option value="warning">WARNING</option>
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74 <option value="info" selected="true">INFO</option>
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75 </param>
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76 </when>
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77 <when value="FALSE"></when>
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78 </conditional>
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79 </section>
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80 </inputs>
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82 <outputs>
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83 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp">
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84 <change_format>
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85 <when input="input_file.ext" value="mgf" format="mgf" />
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86 <when input="input_file.ext" value="json" format="json" />
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87 <when input="input_file.ext" value="csv" format="csv" />
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88 <when input="input_file.ext" value="tsv" format="tsv" />
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89 <when input="input_file.ext" value="xlsx" format="xlsx" />
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90 </change_format>
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91 </data>
0
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92 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
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93 <filter>options['logging']['output_log']</filter>
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94 </data>
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95 </outputs>
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96
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97 <tests>
10
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98 <test expect_num_outputs="2">
0
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99 <param name="input_file" value="sample.msp" ftype="msp" />
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100 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
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101 <output name="output_file" file="sample_out.msp" ftype="msp"/>
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102 </test>
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103 </tests>
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104
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105 <help>
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106 <![CDATA[
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107 @HELP@
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108 ]]>
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109 </help>
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110
10
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111 <citations>
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112 <citation type="doi">https://doi.org/10.21105/joss.04494</citation>
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113 </citations>
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114
0
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115 </tool>