Mercurial > repos > recetox > msmetaenhancer

comparison 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
comparison
equal deleted inserted replaced
2:8338640d8676 3:f387ebd6b734
1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
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>
17 <configfiles> 17 <configfiles>
18 <configfile name="msmetaenhancer_python_cli"> 18 <configfile name="msmetaenhancer_python_cli">
19 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \ 19 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
20 --input_file "$input_file" \ 20 --input_file "$input_file" \
21 --output_file "$output_file" \ 21 --output_file "$output_file" \
22 #if $options.output_log: 22 #if $options.logging.output_log:
23 --log_file "$log_file"\ 23 --log_file "$log_file" \
24 --log_level "$options.logging.log_level" \
24 #end if 25 #end if
25 #if len($ordered_jobs) != 0: 26 #if len($ordered_jobs) != 0:
26 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + "," 27 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
27 #else: 28 #else:
28 #set ordered_jobs = "" 29 #set ordered_jobs = ""
49 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true"> 50 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
50 <expand macro="job_options" /> 51 <expand macro="job_options" />
51 </param> 52 </param>
52 53
53 <section name="options" title="Options"> 54 <section name="options" title="Options">
54 <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE" 55 <conditional name="logging">
55 checked="false" help="Preserve a log with details about the annotation process."/> 56 <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
57 checked="false" help="Preserve a log with details about the annotation process."/>
58 <when value="TRUE">
59 <param name="log_level" type="select" label="Log level"
60 help="Severity of log messages present in the log file.">
61 <option value="error">ERROR</option>
62 <option value="warning">WARNING</option>
63 <option value="info" selected="true">INFO</option>
64 </param>
65 </when>
66 </conditional>
56 </section> 67 </section>
57 </inputs> 68 </inputs>
58 69
59 <outputs> 70 <outputs>
60 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" /> 71 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
61 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt"> 72 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
62 <filter>options['output_log']</filter> 73 <filter>options['logging']['output_log']</filter>
63 </data> 74 </data>
64 </outputs> 75 </outputs>
65 76
66 <tests> 77 <tests>
67 <test> 78 <test>