Mercurial > repos > galaxyp > thermo_raw_file_converter
changeset 0:00c4b28150bd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit f211dc8467604ef106cc85b4c68aec5707a24c6d
| author | galaxyp |
|---|---|
| date | Fri, 14 Sep 2018 18:04:17 -0400 |
| parents | |
| children | 15d2a50acaeb |
| files | test-data/fake_input.txt thermo_converter.xml |
| diffstat | 2 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_input.txt Fri Sep 14 18:04:17 2018 -0400 @@ -0,0 +1,1 @@ +This is a fake input, I was not able to find a very small RAW file.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/thermo_converter.xml Fri Sep 14 18:04:17 2018 -0400 @@ -0,0 +1,56 @@ +<tool id="thermo_raw_file_converter" name="Thermo" version="0.0.1"> + <description>RAW file converter (beta)</description> + <requirements> + <requirement type="package" version="0.0.2018.09.07">ThermoRawFileParser</requirement> + </requirements> + <command> +<![CDATA[ + +ln -s '$input' ./input.raw && + +ThermoRawFileParser.sh + -i=input.raw + -o=./ + -f=1 + #if $metadata: + --metadata=1 + #end if +]]> + </command> + <inputs> + <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" /> + <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False" + label="Output metadata" help="" /> + </inputs> + <outputs> + <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}" /> + <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata"> + <filter>metadata</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="fake_input.txt"/> + <assert_command> + <has_text text="ThermoRawFileParser.sh"/> + </assert_command> + </test> + </tests> + <help> +<![CDATA[ + +Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project. + +]]> + </help> + <citations> + <citation type="bibtex">@misc{Galaxy Proteomics Tools, + author = {Niels Hulstaert, et al.}, + title = {Galaxy Proteomics Tools}, + publisher = {GitHub}, + journal = {GitHub repository}, + year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}} + </citation> + </citations> +</tool> +