Mercurial > repos > recetox > aplcms_hybrid
changeset 1:87f5cf0baf34 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
| author | recetox |
|---|---|
| date | Tue, 26 Jan 2021 17:11:11 +0000 |
| parents | d3d9ba599d51 |
| children | a1439454fe7f |
| files | aplcms_hybrid.xml aplcms_macros.xml |
| diffstat | 2 files changed, 13 insertions(+), 12 deletions(-) [+] |
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--- a/aplcms_hybrid.xml Sun Oct 18 10:36:05 2020 +0000 +++ b/aplcms_hybrid.xml Tue Jan 26 17:11:11 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy1"> +<tool id="aplcms_hybrid" name="apLCMS - Hybrid" version="@TOOL_VERSION@+galaxy2"> <macros> <import>aplcms_macros.xml</import> </macros> @@ -6,12 +6,12 @@ <expand macro="requirements" /> <command detect_errors="aggressive"><![CDATA[ - #set file_str = str('", "').join([str($f) for $f in $files]) + #set file_str = str("', '").join([str($f) for $f in $files]) Rscript - -e 'x <- apLCMS::hybrid( - files = c("$file_str"), - known_table = apLCMS::load_known_table_from_hdf("$known_table"), + -e "x <- apLCMS::hybrid( + files = c('$file_str'), + 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, @@ -19,9 +19,9 @@ baseline_correct = $noise_filtering.baseline_correct, baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, intensity_weighted = $noise_filtering.intensity_weighted, - shape_model = "$feature_detection.shape_model", + shape_model = '$feature_detection.shape_model', BIC_factor = $feature_detection.BIC_factor, - peak_estim_method = "$feature_detection.peak_estim_method", + peak_estim_method = '$feature_detection.peak_estim_method', min_bandwidth = $feature_detection.min_bandwidth, max_bandwidth = $feature_detection.max_bandwidth, sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), @@ -36,10 +36,11 @@ recover_mz_range = $weak_signal_recovery.recover_mz_range, recover_chr_range = $weak_signal_recovery.recover_chr_range, use_observed_range = $weak_signal_recovery.use_observed_range, - recover_min_count = $weak_signal_recovery.recover_min_count - )' - -e 'apLCMS::save_peaks_to_hdf("$peaks", x)' - -e 'apLCMS::save_known_table_to_hdf("$updated_known_table", x\$updated_known_table)' + recover_min_count = $weak_signal_recovery.recover_min_count, + cluster = as.integer(\${GALAXY_SLOTS:-1}) + )" + -e "apLCMS::save_peaks_to_hdf('$peaks', x)" + -e "apLCMS::save_known_table_to_hdf('$updated_known_table', x\\$updated_known_table)" ## NOTE the double \\ because we want cheetah and bash to ignore the $ character ]]></command> <expand macro="inputs">
--- a/aplcms_macros.xml Sun Oct 18 10:36:05 2020 +0000 +++ b/aplcms_macros.xml Tue Jan 26 17:11:11 2021 +0000 @@ -3,7 +3,7 @@ <xml name="requirements"> <requirements> - <container type="docker">recetox/aplcms:6.6.6-recetox1</container> + <container type="docker">recetox/aplcms:6.6.6-recetox2</container> </requirements> </xml>