Mercurial > repos > recetox > recetox_aplcms_hybrid
diff aplcms_hybrid.xml @ 3:bb4ffaeba411 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 1852a90740a2e1e98f576d68164100c46daaf71a"
| author | recetox |
|---|---|
| date | Wed, 07 Oct 2020 16:07:23 +0000 |
| parents | 30b1888f985a |
| children |
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--- a/aplcms_hybrid.xml Thu Sep 24 07:23:39 2020 +0000 +++ b/aplcms_hybrid.xml Wed Oct 07 16:07:23 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="recetox_aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy0"> +<tool id="recetox_aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy1"> <macros> <import>aplcms_macros.xml</import> </macros> @@ -11,7 +11,7 @@ Rscript -e 'x <- apLCMS::hybrid( files = c("$file_str"), - known_table = rhdf5::h5read("$known_table", "aplcms_known_table"), + known_table = apLCMS::load_known_table_from_hdf("$known_table"), min_exp = $noise_filtering.min_exp, min_pres = $noise_filtering.min_pres, min_run = $noise_filtering.min_run, @@ -38,13 +38,8 @@ use_observed_range = $weak_signal_recovery.use_observed_range, recover_min_count = $weak_signal_recovery.recover_min_count )' - -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")' - -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")' - -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")' - -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")' - -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")' - -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")' - -e 'rhdf5::h5write(x\$updated_known_table, "$updated_known_table", "aplcms_known_table")' + -e 'apLCMS::save_peaks_to_hdf("$peaks", x)' + -e 'apLCMS::save_known_table_to_hdf("$updated_known_table", x\$updated_known_table)' ]]></command> <expand macro="inputs"> @@ -60,6 +55,14 @@ <data name="updated_known_table" format="h5" /> </outputs> + <tests> + <test> + <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> + <param name="known_table" value="known_table.h5" ftype="h5"/> + <output name="peaks" file="peaks_hybrid.h5" ftype="h5" compare="sim_size" delta="1000"/> + </test> + </tests> + <help> This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically detected features on the same machinery to help detect and quantify lower-intensity peaks.