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comparison 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
comparison
equal deleted inserted replaced
9:90745ecc5e9f 10:3e2cb0bc6959
1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy3">
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>
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>