Mercurial > repos > recetox > msmetaenhancer
comparison msmetaenhancer.xml @ 13:f4a90c68e2de draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 1d1ecf792f5ea1c8a8f443dd1c3f55c810c5b00d
| author | recetox |
|---|---|
| date | Mon, 27 May 2024 12:40:12 +0000 |
| parents | 5de89437323f |
| children |
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| 12:5de89437323f | 13:f4a90c68e2de |
|---|---|
| 1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1"> | 1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0" profile="21.09"> |
| 2 <description>annotate MS data</description> | 2 <description>annotate MS data</description> |
| 3 | 3 |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 11 | 11 |
| 12 <requirements> | 12 <requirements> |
| 13 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement> | 13 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement> |
| 14 </requirements> | 14 </requirements> |
| 15 | 15 |
| 16 <command detect_errors="exit_code"><![CDATA[ | |
| 17 sh ${msmetaenhancer_python_cli} | |
| 18 ]]> </command> | |
| 19 | |
| 16 <environment_variables> | 20 <environment_variables> |
| 17 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> | 21 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> |
| 18 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> | 22 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> |
| 19 </environment_variables> | 23 </environment_variables> |
| 20 | |
| 21 <command detect_errors="exit_code"><![CDATA[ | |
| 22 sh ${msmetaenhancer_python_cli} | |
| 23 ]]> </command> | |
| 24 | 24 |
| 25 <configfiles> | 25 <configfiles> |
| 26 <configfile name="msmetaenhancer_python_cli"> | 26 <configfile name="msmetaenhancer_python_cli"> |
| 27 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \ | 27 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \ |
| 28 --input_file "$input_file" \ | 28 --input_file "$input_file" \ |
| 29 --file_format "$input_file.ext" \ | 29 --file_format "$input_file.ext" \ |
| 30 --output_file "$output_file" \ | 30 --output_file "$output_file" \ |
| 31 #if $options.logging.output_log: | 31 #if $options.logging.output_log == "TRUE": |
| 32 --log_file "$log_file" \ | 32 --log_file "$log_file" \ |
| 33 --log_level "$options.logging.log_level" \ | 33 --log_level "$options.logging.log_level" \ |
| 34 #end if | 34 #end if |
| 35 #if len($ordered_jobs) != 0: | 35 #if len($ordered_jobs) != 0: |
| 36 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + "," | 36 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + "," |
| 60 <expand macro="job_options" /> | 60 <expand macro="job_options" /> |
| 61 </param> | 61 </param> |
| 62 | 62 |
| 63 <section name="options" title="Options"> | 63 <section name="options" title="Options"> |
| 64 <conditional name="logging"> | 64 <conditional name="logging"> |
| 65 <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE" | 65 <param label="Save the log file" name="output_log" type="select" help="Preserve a log with details about the annotation process."> |
| 66 checked="false" help="Preserve a log with details about the annotation process."/> | 66 <option value="FALSE" selected="true">FALSE</option> |
| 67 <option value="TRUE">TRUE</option> | |
| 68 </param> | |
| 67 <when value="TRUE"> | 69 <when value="TRUE"> |
| 68 <param name="log_level" type="select" label="Log level" | 70 <param name="log_level" type="select" label="Log level" |
| 69 help="Severity of log messages present in the log file."> | 71 help="Severity of log messages present in the log file."> |
| 70 <option value="error">ERROR</option> | 72 <option value="error">ERROR</option> |
| 71 <option value="warning">WARNING</option> | 73 <option value="warning">WARNING</option> |
| 72 <option value="info" selected="true">INFO</option> | 74 <option value="info" selected="true">INFO</option> |
| 73 </param> | 75 </param> |
| 74 </when> | 76 </when> |
| 77 <when value="FALSE"></when> | |
| 75 </conditional> | 78 </conditional> |
| 76 </section> | 79 </section> |
| 77 </inputs> | 80 </inputs> |
| 78 | 81 |
| 79 <outputs> | 82 <outputs> |
| 80 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp"> | 83 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp"> |
| 81 <change_format> | 84 <change_format> |
| 82 <when input="input_file.ext" value="mgf" format="mgf" /> | 85 <when input="input_file.ext" value="mgf" format="mgf" /> |
| 83 <when input="input_file.ext" value="json" format="json" /> | 86 <when input="input_file.ext" value="json" format="json" /> |
| 84 <when input="input_file.ext" value="csv" format="csv" /> | 87 <when input="input_file.ext" value="csv" format="tsv" /> |
| 85 <when input="input_file.ext" value="tsv" format="tsv" /> | 88 <when input="input_file.ext" value="tsv" format="tsv" /> |
| 86 <when input="input_file.ext" value="xlsx" format="xlsx" /> | 89 <when input="input_file.ext" value="xlsx" format="xlsx" /> |
| 87 </change_format> | 90 </change_format> |
| 88 </data> | 91 </data> |
| 89 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt"> | 92 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt"> |
| 90 <filter>options['logging']['output_log']</filter> | 93 <filter>options['logging']['output_log']</filter> |
| 91 </data> | 94 </data> |
| 92 </outputs> | 95 </outputs> |
| 93 | 96 |
| 94 <tests> | 97 <tests> |
| 95 <test> | 98 <test expect_num_outputs="2"> |
| 96 <param name="input_file" value="sample.msp" ftype="msp" /> | 99 <param name="input_file" value="sample.msp" ftype="msp" /> |
| 97 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> | 100 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> |
| 98 <output name="output_file" file="sample_out.msp" ftype="msp"/> | 101 <output name="output_file" file="sample_out.msp" ftype="msp"/> |
| 99 </test> | 102 </test> |
| 100 </tests> | 103 </tests> |
| 103 <![CDATA[ | 106 <![CDATA[ |
| 104 @HELP@ | 107 @HELP@ |
| 105 ]]> | 108 ]]> |
| 106 </help> | 109 </help> |
| 107 | 110 |
| 111 <citations> | |
| 112 <citation type="doi">https://doi.org/10.21105/joss.04494</citation> | |
| 113 </citations> | |
| 114 | |
| 108 </tool> | 115 </tool> |