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comparison msmetaenhancer.xml @ 0:ce612a11b455 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
author recetox
date Tue, 22 Mar 2022 15:33:37 +0000
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children 8338640d8676
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-1:000000000000 0:ce612a11b455
1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
2 <description>annotate MS data</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="creator"/>
8
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
11 </requirements>
12
13 <command detect_errors="exit_code"><![CDATA[
14 sh ${msmetaenhancer_python_cli}
15 ]]> </command>
16
17 <configfiles>
18 <configfile name="msmetaenhancer_python_cli">
19 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
20 --input_file "$input_file" \
21 --output_file "$output_file" \
22 #if $options.output_log:
23 --log_file "$log_file"\
24 #end if
25 #if len($ordered_jobs) != 0:
26 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
27 #else:
28 #set ordered_jobs = ""
29 #end if
30 #if $jobs != 'None':
31 #set random_jobs = str($jobs)
32 #else:
33 #set random_jobs = ""
34 #end if
35 #set all_jobs = str($ordered_jobs) + str($random_jobs)
36 --jobs "$all_jobs"
37 </configfile>
38 </configfiles>
39
40 <inputs>
41 <param label="Input spectra dataset" name="input_file" type="data" format="msp" />
42
43 <repeat name="ordered_jobs" title="Ordered conversions">
44 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
45 <expand macro="job_options" />
46 </param>
47 </repeat>
48
49 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
50 <expand macro="job_options" />
51 </param>
52
53 <section name="options" title="Options">
54 <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
55 checked="false" help="Preserve a log with details about the annotation process."/>
56 </section>
57 </inputs>
58
59 <outputs>
60 <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">
62 <filter>options['output_log']</filter>
63 </data>
64 </outputs>
65
66 <tests>
67 <test>
68 <param name="input_file" value="sample.msp" ftype="msp" />
69 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
70 <output name="output_file" file="sample_out.msp" ftype="msp"/>
71 </test>
72 </tests>
73
74 <help>
75 <![CDATA[
76 @HELP@
77 ]]>
78 </help>
79
80 </tool>