Mercurial > repos > recetox > msmetaenhancer
diff msmetaenhancer.xml @ 14:646ef66527da draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 187cd20cfa1502639fa2678dbcd69d2f3158d436
| author | recetox |
|---|---|
| date | Thu, 29 May 2025 11:21:26 +0000 |
| parents | b5467dead5b1 |
| children | 560053b805d2 |
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--- a/msmetaenhancer.xml Fri May 31 07:51:40 2024 +0000 +++ b/msmetaenhancer.xml Thu May 29 11:21:26 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1" profile="21.09"> +<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>annotate MS data</description> <macros> @@ -26,7 +26,11 @@ <configfile name="msmetaenhancer_python_cli"> python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \ --input_file "$input_file" \ + #if $input_file.ext == "tabular": + --file_format "tsv" \ + #else --file_format "$input_file.ext" \ + #end if --output_file "$output_file" \ #if $options.logging.output_log == "TRUE": --log_file "$log_file" \ @@ -48,7 +52,7 @@ </configfiles> <inputs> - <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tsv,xlsx" /> + <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tabular,xlsx" /> <repeat name="ordered_jobs" title="Ordered conversions"> <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true"> @@ -80,13 +84,11 @@ </inputs> <outputs> - <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp"> + <data label="MSMetaEnhancer on ${on_string}" name="output_file" format_source="input_file"> <change_format> - <when input="input_file.ext" value="mgf" format="mgf" /> - <when input="input_file.ext" value="json" format="json" /> - <when input="input_file.ext" value="csv" format="tsv" /> - <when input="input_file.ext" value="tsv" format="tsv" /> - <when input="input_file.ext" value="xlsx" format="xlsx" /> + <when input="input_file.ext" value="csv" format="tabular" /> + <when input="input_file.ext" value="tsv" format="tabular" /> + <when input="input_file.ext" value="xlsx" format="tabular" /> </change_format> </data> <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt"> @@ -100,6 +102,16 @@ <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> <output name="output_file" file="sample_out.msp" ftype="msp"/> </test> + <test expect_num_outputs="2"> + <param name="input_file" value="msme_sample.tsv" ftype="tsv" /> + <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> + <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/> + </test> + <test expect_num_outputs="2"> + <param name="input_file" value="msme_sample.tsv" ftype="tabular" /> + <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/> + <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/> + </test> </tests> <help>