Mercurial > repos > recetox > recetox_aplcms_hybrid
diff recetox_aplcms_hybrid.xml @ 10:27853894eeac draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
| author | recetox |
|---|---|
| date | Thu, 21 Oct 2021 15:03:51 +0000 |
| parents | d62f052efae6 |
| children | ab2b7948bdb7 |
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--- a/recetox_aplcms_hybrid.xml Tue Oct 05 13:13:20 2021 +0000 +++ b/recetox_aplcms_hybrid.xml Thu Oct 21 15:03:51 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy1"> +<tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy2"> <description>generate a feature table from LC/MS spectra</description> <macros> <import>recetox_aplcms_macros.xml</import> @@ -25,6 +25,7 @@ pairing_file = '${feature_known_table_pairing}', aligned_file = '${aligned_feature_sample_table}', recovered_file = '${recovered_feature_sample_table}', + out_format = '$output_format.out_format', min_exp = $noise_filtering.min_exp, min_pres = $noise_filtering.min_pres, min_run = $noise_filtering.min_run, @@ -61,6 +62,7 @@ <expand macro="feature_detection" /> <expand macro="peak_alignment" /> <expand macro="weak_signal_recovery" /> + <expand macro="output_format" /> </expand> <outputs> @@ -75,6 +77,14 @@ <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" /> </test> + <test> + <param name="known_table" value="known_table.parquet" ftype="parquet" /> + <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> + <section name="output_format"> + <param name="out_format" value="recetox" /> + </section> + <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet" /> + </test> </tests> <help>