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comparison msmetaenhancer.xml @ 15:560053b805d2 draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:44:57 +0000
parents 646ef66527da
children
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14:646ef66527da 15:560053b805d2
1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0" profile="21.09"> 1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy2" profile="23.0">
2 <description>annotate MS data</description> 2 <description>collect and convert chemical identifiers in tables or MS libraries</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="creator"/> 7 <expand macro="creator"/>
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[ 16 <required_files>
17 sh ${msmetaenhancer_python_cli} 17 <include path="msmetaenhancer_wrapper.py"/>
18 </required_files>
19
20 <command detect_errors="aggressive"><![CDATA[
21 python3 '${__tool_directory__}/msmetaenhancer_wrapper.py'
22 --input_file '$input_file'
23 #if $input_file.ext == "tabular":
24 --file_format 'tsv'
25 #else
26 --file_format '$input_file.ext'
27 #end if
28 --output_file '$output_file'
29 #if $options.logging.output_log == "TRUE":
30 --log_file '$log_file'
31 --log_level '$options.logging.log_level'
32 #end if
33 #if len($ordered_jobs) != 0:
34 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
35 #else:
36 #set ordered_jobs = ""
37 #end if
38 #if $jobs != 'None':
39 #set random_jobs = str($jobs)
40 #else:
41 #set random_jobs = ""
42 #end if
43 #set all_jobs = str($ordered_jobs) + str($random_jobs)
44 --jobs '$all_jobs'
18 ]]> </command> 45 ]]> </command>
19 46
20 <environment_variables> 47 <environment_variables>
21 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> 48 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
22 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> 49 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
23 </environment_variables> 50 </environment_variables>
24
25 <configfiles>
26 <configfile name="msmetaenhancer_python_cli">
27 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
28 --input_file "$input_file" \
29 #if $input_file.ext == "tabular":
30 --file_format "tsv" \
31 #else
32 --file_format "$input_file.ext" \
33 #end if
34 --output_file "$output_file" \
35 #if $options.logging.output_log == "TRUE":
36 --log_file "$log_file" \
37 --log_level "$options.logging.log_level" \
38 #end if
39 #if len($ordered_jobs) != 0:
40 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
41 #else:
42 #set ordered_jobs = ""
43 #end if
44 #if $jobs != 'None':
45 #set random_jobs = str($jobs)
46 #else:
47 #set random_jobs = ""
48 #end if
49 #set all_jobs = str($ordered_jobs) + str($random_jobs)
50 --jobs "$all_jobs"
51 </configfile>
52 </configfiles>
53 51
54 <inputs> 52 <inputs>
55 <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tabular,xlsx" /> 53 <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tabular,xlsx" />
56 54
57 <repeat name="ordered_jobs" title="Ordered conversions"> 55 <repeat name="ordered_jobs" title="Ordered conversions">
90 <when input="input_file.ext" value="tsv" format="tabular" /> 88 <when input="input_file.ext" value="tsv" format="tabular" />
91 <when input="input_file.ext" value="xlsx" format="tabular" /> 89 <when input="input_file.ext" value="xlsx" format="tabular" />
92 </change_format> 90 </change_format>
93 </data> 91 </data>
94 <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">
95 <filter>options['logging']['output_log']</filter> 93 <filter>options['logging']['output_log'] == 'TRUE'</filter>
96 </data> 94 </data>
97 </outputs> 95 </outputs>
98 96
99 <tests> 97 <tests>
100 <test expect_num_outputs="2"> 98 <test expect_num_outputs="2">
101 <param name="input_file" value="sample.msp" ftype="msp" /> 99 <param name="input_file" value="sample.msp" ftype="msp" />
102 <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"/>
101 <section name="options">
102 <conditional name="logging">
103 <param name="output_log" value="TRUE"/>
104 </conditional>
105 </section>
103 <output name="output_file" file="sample_out.msp" ftype="msp"/> 106 <output name="output_file" file="sample_out.msp" ftype="msp"/>
107 <output name="log_file" ftype="txt">
108 <assert_contents>
109 <has_text text=""/>
110 </assert_contents>
111 </output>
104 </test> 112 </test>
105 <test expect_num_outputs="2"> 113 <test expect_num_outputs="1">
106 <param name="input_file" value="msme_sample.tsv" ftype="tsv" /> 114 <param name="input_file" value="msme_sample.tsv" ftype="tsv" />
107 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> 115 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
108 <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/> 116 <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/>
109 </test> 117 </test>
110 <test expect_num_outputs="2"> 118 <test expect_num_outputs="1">
111 <param name="input_file" value="msme_sample.tsv" ftype="tabular" /> 119 <param name="input_file" value="msme_sample.tsv" ftype="tabular" />
112 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> 120 <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
113 <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/> 121 <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/>
114 </test> 122 </test>
115 </tests> 123 </tests>