Mercurial > repos > galaxyp > thermo_raw_file_converter
comparison thermo_converter.xml @ 0:00c4b28150bd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
author | galaxyp |
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date | Fri, 14 Sep 2018 18:04:17 -0400 |
parents | |
children | 15d2a50acaeb |
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1 <tool id="thermo_raw_file_converter" name="Thermo" version="0.0.1"> | |
2 <description>RAW file converter (beta)</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.0.2018.09.07">ThermoRawFileParser</requirement> | |
5 </requirements> | |
6 <command> | |
7 <![CDATA[ | |
8 | |
9 ln -s '$input' ./input.raw && | |
10 | |
11 ThermoRawFileParser.sh | |
12 -i=input.raw | |
13 -o=./ | |
14 -f=1 | |
15 #if $metadata: | |
16 --metadata=1 | |
17 #end if | |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" /> | |
22 <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False" | |
23 label="Output metadata" help="" /> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}" /> | |
27 <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata"> | |
28 <filter>metadata</filter> | |
29 </data> | |
30 </outputs> | |
31 <tests> | |
32 <test> | |
33 <param name="input" value="fake_input.txt"/> | |
34 <assert_command> | |
35 <has_text text="ThermoRawFileParser.sh"/> | |
36 </assert_command> | |
37 </test> | |
38 </tests> | |
39 <help> | |
40 <![CDATA[ | |
41 | |
42 Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project. | |
43 | |
44 ]]> | |
45 </help> | |
46 <citations> | |
47 <citation type="bibtex">@misc{Galaxy Proteomics Tools, | |
48 author = {Niels Hulstaert, et al.}, | |
49 title = {Galaxy Proteomics Tools}, | |
50 publisher = {GitHub}, | |
51 journal = {GitHub repository}, | |
52 year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}} | |
53 </citation> | |
54 </citations> | |
55 </tool> | |
56 |