diff --git a/tools/mfassignr/macros.xml b/tools/mfassignr/macros.xml index f24d7098..5b1742d8 100644 --- a/tools/mfassignr/macros.xml +++ b/tools/mfassignr/macros.xml @@ -1,5 +1,5 @@ - 1.1.1 + 1.1.2 r-mfassignr @@ -208,26 +208,6 @@ - - - - - - - - - - - diff --git a/tools/mfassignr/mfassignr_findRecalSeries.xml b/tools/mfassignr/mfassignr_findRecalSeries.xml index 8ce36026..b0a4aeea 100644 --- a/tools/mfassignr/mfassignr_findRecalSeries.xml +++ b/tools/mfassignr/mfassignr_findRecalSeries.xml @@ -12,53 +12,44 @@ - + + dplyr::rename(Series = series) - + result <- MFAssignR::FindRecalSeriesSimple(df) |> dplyr::slice(-1) write.table(result, file="$final_series", sep="\t", row.names=FALSE) ]]> + - + + + - - - - - - - + + @FINDRECALSERIES_HELP@ @GENERAL_HELP@ + diff --git a/tools/mfassignr/mfassignr_recal.xml b/tools/mfassignr/mfassignr_recal.xml index e5588a27..43eb095f 100644 --- a/tools/mfassignr/mfassignr_recal.xml +++ b/tools/mfassignr/mfassignr_recal.xml @@ -71,13 +71,13 @@ - + - + diff --git a/tools/mfassignr/mfassignr_snplot.xml b/tools/mfassignr/mfassignr_snplot.xml index a7756094..10e0dde9 100644 --- a/tools/mfassignr/mfassignr_snplot.xml +++ b/tools/mfassignr/mfassignr_snplot.xml @@ -20,8 +20,8 @@ df = read.delim("$input_file", sep="\t"), cut = cut, mass = $mass, - window.x = $window_x, - window.y = $window_y + mass_window = $window_x, + abundance_window = $window_y ) ggplot2::ggsave(filename = "SNplot.png", SNplot) diff --git a/tools/mfassignr/test-data/findrecalseries/selected_series_simple.tabular b/tools/mfassignr/test-data/findrecalseries/selected_series_simple.tabular new file mode 100644 index 00000000..77718201 --- /dev/null +++ b/tools/mfassignr/test-data/findrecalseries/selected_series_simple.tabular @@ -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 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--- a/tools/mfassignr/test-data/isofiltr/iso_out.tabular +++ b/tools/mfassignr/test-data/isofiltr/iso_out.tabular @@ -451,7 +451,6 @@ 198.11278512548 23941071.6060839 562.734801542562 "S34" 198.120268298499 74544575.0339617 418.233755768477 "C13" 198.120642908004 35897295.2062584 503.129833851604 "C13" -198.1314942 129610721.726295 310.984037232271 "C13" 198.156573332388 16685411.9229059 723.914434277142 "C13" 198.193260481641 1058393.75378714 668.988615693481 "C13" 199.075318147071 3330663.8762492 526.736331724065 "S34" @@ -737,7 +736,7 @@ 233.13681280613 11601217.5677659 629.635903861914 "S34" 233.137767293096 106145239.684739 497.079485697109 "S34" 233.156873358746 953506796.058272 221.997813102967 "C13" -233.164518791019 2377175.5732822 351.160198568355 "2C13_S34" +233.164518791019 2377175.5732822 351.160198568355 "C13_S34" 233.17264326984 26759543.4346631 704.591349841955 "C13" 233.193187725279 6279641.29710976 432.048268560514 "C13" 234.007662297674 3130283.5615464 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