Mercurial > repos > recetox > msmetaenhancer

annotate msmetaenhancer.xml @ 3:f387ebd6b734 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"
author recetox
date Fri, 06 May 2022 12:21:30 +0000
parents 8338640d8676
children a2bf129850ea
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1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
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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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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
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11 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 sh ${msmetaenhancer_python_cli}
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15 ]]> </command>
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17 <configfiles>
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18 <configfile name="msmetaenhancer_python_cli">
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19 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
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20 --input_file "$input_file" \
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21 --output_file "$output_file" \
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22 #if $options.logging.output_log:
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23 --log_file "$log_file" \
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24 --log_level "$options.logging.log_level" \
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25 #end if
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26 #if len($ordered_jobs) != 0:
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27 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
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28 #else:
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29 #set ordered_jobs = ""
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30 #end if
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31 #if $jobs != 'None':
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32 #set random_jobs = str($jobs)
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33 #else:
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34 #set random_jobs = ""
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35 #end if
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36 #set all_jobs = str($ordered_jobs) + str($random_jobs)
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37 --jobs "$all_jobs"
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38 </configfile>
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39 </configfiles>
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41 <inputs>
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42 <param label="Input spectra dataset" name="input_file" type="data" format="msp" />
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44 <repeat name="ordered_jobs" title="Ordered conversions">
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45 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
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46 <expand macro="job_options" />
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47 </param>
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48 </repeat>
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49
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50 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
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51 <expand macro="job_options" />
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52 </param>
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53
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54 <section name="options" title="Options">
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55 <conditional name="logging">
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56 <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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57 checked="false" help="Preserve a log with details about the annotation process."/>
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58 <when value="TRUE">
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59 <param name="log_level" type="select" label="Log level"
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60 help="Severity of log messages present in the log file.">
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61 <option value="error">ERROR</option>
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62 <option value="warning">WARNING</option>
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63 <option value="info" selected="true">INFO</option>
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64 </param>
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65 </when>
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66 </conditional>
0
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67 </section>
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68 </inputs>
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70 <outputs>
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71 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
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72 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
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73 <filter>options['logging']['output_log']</filter>
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74 </data>
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75 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input_file" value="sample.msp" ftype="msp" />
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80 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
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81 <output name="output_file" file="sample_out.msp" ftype="msp"/>
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82 </test>
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83 </tests>
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84
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85 <help>
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86 <![CDATA[
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87 @HELP@
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88 ]]>
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89 </help>
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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90
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
91 </tool>