# HG changeset patch
# User recetox
# Date 1730449162 0
# Node ID a7a823839ae3989f259d427c69bb18c738eded42
# Parent  634ae07958a2615a7fc5c15f19790100a05a7461
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030

diff -r 634ae07958a2 -r a7a823839ae3 macros.xml
--- a/macros.xml	Tue Oct 22 07:25:03 2024 +0000
+++ b/macros.xml	Fri Nov 01 08:19:22 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"/>
diff -r 634ae07958a2 -r a7a823839ae3 test-data/findrecalseries/selected_series_simple.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/findrecalseries/selected_series_simple.tabular	Fri Nov 01 08:19:22 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
diff -r 634ae07958a2 -r a7a823839ae3 test-data/isofiltr/iso_out.tabular
--- a/test-data/isofiltr/iso_out.tabular	Tue Oct 22 07:25:03 2024 +0000
+++ b/test-data/isofiltr/iso_out.tabular	Fri Nov 01 08:19:22 2024 +0000
@@ -451,7 +451,6 @@
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@@ -737,7 +736,7 @@
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@@ -1097,6 +1098,7 @@
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diff -r 634ae07958a2 -r a7a823839ae3 test-data/isofiltr/mono_out.tabular
--- a/test-data/isofiltr/mono_out.tabular	Tue Oct 22 07:25:03 2024 +0000
+++ b/test-data/isofiltr/mono_out.tabular	Fri Nov 01 08:19:22 2024 +0000
@@ -1947,6 +1947,7 @@
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 463.088858696242	4487114.62368511	454.75048830377
 463.128985480723	1702608.97878654	868.4503548
@@ -8638,10 +8597,8 @@
 466.125835862037	524107.673555569	341.577562914833
 466.128538697439	481693.348890603	434.198240393334
 466.132590066552	97348450.4885318	438.246805963253
-466.1380001	1357017.02659344	990.60214300181
 466.170404467096	93662172.2590393	461.948838651162
 466.19471954491	92080235.6799811	536.453165479317
-466.205524763253	67785235.81	505.6724337
 466.225788920902	14066264.5763932	641.8135605
 466.227136143072	73006100.8548653	390.6806084932
 466.227138051183	464338840.717891	475.749897987666
@@ -8856,13 +8813,10 @@
 479.18956565721	111502471.165006	444.343418124967
 479.205052452451	7648210.56259654	598.079211813883
 479.223354564125	15457223.7910889	713.852207245619
-479.226166444781	23818979.6922602	495.925430246591
-479.226167330729	39693650.03	531.184191332583
 479.228983780887	14895294.6022417	587.344023791244
 479.247284515764	177394412.931401	532.673064340043
 479.296566131505	21964307.9044292	731.85520874306
 479.3092372	31904404.07	631.273216553137
-479.312050732579	3207024.51611706	406.486448037546
 479.334587436396	10737427.1841608	742.966237195642
 480.149584476662	126887128.223587	216.957207158715
 480.186294338078	235747234.340003	437.016099676598
@@ -9037,7 +8991,6 @@
 490.206061622032	105884941.92294	589.559016
 490.229369128826	44393551.243901	852.763324693888
 490.236640212202	371470428.295075	149.8837309
-490.24101462448	2461536.37738184	151.518056081121
 490.243927997779	3918842.56299929	460.908532847505
 490.246845913072	9644772.448	706.92319362724
 490.258496152149	9492623.14840407	564.222679250139
diff -r 634ae07958a2 -r a7a823839ae3 test-data/snplot/plot.png
Binary file test-data/snplot/plot.png has changed