Mercurial > repos > recetox > mfassignr_mfassign
changeset 6:22c80f584bb1 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030
| author | recetox |
|---|---|
| date | Fri, 01 Nov 2024 08:19:30 +0000 |
| parents | 0492fff60960 |
| children | |
| files | macros.xml test-data/findrecalseries/selected_series_simple.tabular test-data/isofiltr/iso_out.tabular test-data/isofiltr/mono_out.tabular test-data/snplot/plot.png |
| diffstat | 5 files changed, 88 insertions(+), 97 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Oct 22 07:25:13 2024 +0000 +++ b/macros.xml Fri Nov 01 08:19:30 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.1.1</token> + <token name="@TOOL_VERSION@">1.1.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement> @@ -208,26 +208,6 @@ </section> </xml> - <xml name="findrecalseries_param"> - <param name="input_file" type="data" format="tabular" label="Input data" - help= "Recalibration series, output from RecalList"/> - <param name="global_min" type="float" label="Global min" value="0" min="0" - help= "A lower bound of the instrument m/z range."/> - <param name="global_max" type="float" label="Global max" value="1000" min="0" - help= "A higher bound of the instrument m/z range."/> - <param name="number_of_combinations" type="integer" label="Number of combinations" - help= "Combinations of how many series should be computed." value="5"/> - <param name="abundance_score_threshold" type="float" label="Abundance score threshold" value="100" - help= "A threshold for filtering abundance score parameter. The series with higher values are better."/> - <param name="peak_distance_threshold" type="float" label="Peak distance threshold" value="2" - help= "A threshold for the peak distance parameter. The closer this value is to 1, the better."/> - <param name="coverage_threshold" type="integer" label="How many % of the m/z range should be covered." - help= "How many % of the m/z range should be covered." value="90"/> - <param name="fill_series" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Whether to return top 10 unique series (TRUE) or series only from the best combination." - help= "If TRUE, top 10 unique series will be returned, otherwise only the series from the best - combination will be returned." value="false"/> - </xml> - <xml name="recal_param"> <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)" help= "Input data frame, the output from MFAssign or MFAssignCHO"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/findrecalseries/selected_series_simple.tabular Fri Nov 01 08:19:30 2024 +0000 @@ -0,0 +1,11 @@ +"Series" "Number.Observed" "Series.Index" "Mass.Range" "Tall.Peak" "Abundance.Score" "Peak.Score" "Peak.Distance" "Series.Score" "Num_Weight" "Abund_weight" "TallP_Weight" "PeakS_Weight" "PeakD_Weight" "Series_Weight" "Total_score" +"O_H_7" 12 39 "131.049-299.236" 131.049175570564 172.333212266955 0.840925082711506 1 1.1 25 20 4.36830585235213 5.79537458644247 7 9.16666666666667 71.3303471054613 +"O7_H_4" 11 40 "233.066-415.268" 359.206083268496 -11.5251682369853 0.136136287521764 1 1.3 22.9166666666667 -1.33754464219376 11.9735361089499 9.31931856239118 7 8.125 57.9969766958139 +"O2_H_11" 5 78 "209.06-391.263" 223.074691790747 132.732152227999 0.540579659159889 1 2.8 10.4166666666667 15.4041290685615 7.43582305969157 7.29710170420056 7 6.08695652173913 53.6406770208594 +"O6_H_7" 9 50 "253.071-407.242" 351.1796217 11.6976374801684 0.213201464774084 2 1.3 18.75 1.35756042915837 11.70598739 8.93399267612958 4 8.125 52.872540495288 +"O10_H_3" 7 59 "381.175-465.268" 409.206584131861 2.6997318710302 0.0702879797813004 2 1 14.5833333333333 0.313315330865898 13.640219471062 9.6485601010935 4 10 52.1854282363548 +"O10_H_4" 9 47 "309.081-491.284" 435.222060757962 4.7511651696338 0.655346847143645 2 1.6 18.75 0.551392863526961 14.5074020252654 6.72326576428178 4 7.27272727272727 51.8047879258014 +"O9_H_6" 10 44 "303.07-499.289" 415.195395703443 -21.7793592335313 0.166622042493807 3 1.5 20.8333333333333 -2.52758698651699 13.8398465234481 9.16688978753096 1 7.5 49.8124826577954 +"O8_H_1" 5 69 "213.061-311.169" 311.16936123622 27.8251864824375 0.198145538844287 1 1.6 10.4166666666667 3.22923087388803 10.3723120412073 9.00927230577856 7 7.27272727272727 47.3002091602679 +"O9_H_9" 7 62 "339.071-479.226" 367.101864488525 -18.5226214411156 0.0271291741355916 2 1.6 14.5833333333333 -2.14962875669292 12.2367288162842 9.86435412932204 4 7.27272727272727 45.8075147949739 +"O10_H_6" 6 66 "319.065-487.254" 431.190612941439 -34.0254140710475 0.137560981917351 1 2.2 12.5 -3.94879357536027 14.3730204313813 9.31219509041325 7 6.47058823529412 45.7070101817284
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