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comparison msmetaenhancer.xml @ 0:053ce79ed564 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
author recetox
date Tue, 11 Jan 2022 15:12:26 +0000
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children 4c328e0e59ab
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-1:000000000000 0:053ce79ed564
1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
2 <description>annotate MS data</description>
3 <options sanitize="False"/>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
9 </requirements>
10 <expand macro="creator"/>
11
12 <command detect_errors="exit_code"><![CDATA[
13 sh ${msmetaenhancer_python_cli}
14 ]]> </command>
15
16 <configfiles>
17 <configfile name="msmetaenhancer_python_cli">
18 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
19 --input_file "$input_file" \
20 --output_file "$output_file" \
21 #if len($ordered_jobs) != 0:
22 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
23 #else:
24 #set ordered_jobs = ""
25 #end if
26 #if $jobs != 'None':
27 #set random_jobs = str($jobs)
28 #else:
29 #set random_jobs = ""
30 #end if
31 #set all_jobs = str($ordered_jobs) + str($random_jobs)
32 --jobs "$all_jobs"
33 </configfile>
34 </configfiles>
35
36 <inputs>
37 <param label="Input spectra dataset" name="input_file" type="data" format="msp" />
38
39 <repeat name="ordered_jobs" title="Ordered conversions">
40 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
41 <expand macro="job_options" />
42 </param>
43 </repeat>
44
45 <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
46 <expand macro="job_options" />
47 </param>
48 </inputs>
49
50 <outputs>
51 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
52 </outputs>
53
54 <tests>
55 <test>
56 <param name="input_file" value="sample.msp" ftype="msp" />
57 <output name="output_file" file="sample_out.msp" ftype="msp"/>
58 </test>
59 </tests>
60
61 <help>
62 <![CDATA[
63 @HELP@
64 ]]>
65 </help>
66
67 </tool>