Mercurial > repos > recetox > msmetaenhancer

comparison msmetaenhancer.xml @ 8:2ada1099f42e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
author recetox
date Thu, 18 May 2023 12:57:50 +0000
parents 37afe368348b
children 90745ecc5e9f
comparison
equal deleted inserted replaced
7:37afe368348b 8:2ada1099f42e
1 <tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy2"> 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>
21 21
22 <configfiles> 22 <configfiles>
23 <configfile name="msmetaenhancer_python_cli"> 23 <configfile name="msmetaenhancer_python_cli">
24 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \ 24 python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
25 --input_file "$input_file" \ 25 --input_file "$input_file" \
26 --file_format "$input_file.ext" \
26 --output_file "$output_file" \ 27 --output_file "$output_file" \
27 #if $options.logging.output_log: 28 #if $options.logging.output_log:
28 --log_file "$log_file" \ 29 --log_file "$log_file" \
29 --log_level "$options.logging.log_level" \ 30 --log_level "$options.logging.log_level" \
30 #end if 31 #end if
42 --jobs "$all_jobs" 43 --jobs "$all_jobs"
43 </configfile> 44 </configfile>
44 </configfiles> 45 </configfiles>
45 46
46 <inputs> 47 <inputs>
47 <param label="Input spectra dataset" name="input_file" type="data" format="msp" /> 48 <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tsv,xlsx" />
48 49
49 <repeat name="ordered_jobs" title="Ordered conversions"> 50 <repeat name="ordered_jobs" title="Ordered conversions">
50 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true"> 51 <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
51 <expand macro="job_options" /> 52 <expand macro="job_options" />
52 </param> 53 </param>
71 </conditional> 72 </conditional>
72 </section> 73 </section>
73 </inputs> 74 </inputs>
74 75
75 <outputs> 76 <outputs>
76 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" /> 77 <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp">
78 <change_format>
79 <when input="input_file.ext" value="mgf" format="mgf" />
80 <when input="input_file.ext" value="json" format="json" />
81 <when input="input_file.ext" value="csv" format="csv" />
82 <when input="input_file.ext" value="tsv" format="tsv" />
83 <when input="input_file.ext" value="xlsx" format="xlsx" />
84 </change_format>
85 </data>
77 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt"> 86 <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
78 <filter>options['logging']['output_log']</filter> 87 <filter>options['logging']['output_log']</filter>
79 </data> 88 </data>
80 </outputs> 89 </outputs>
81 90