# HG changeset patch
# User recetox
# Date 1730449180 0
# Node ID 1b4881c150ccdfb2a887d310e72f271a4ccaa317
# Parent  18e13043167d68a14176298c4d9c650b94def040
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030

diff -r 18e13043167d -r 1b4881c150cc macros.xml
--- a/macros.xml	Tue Oct 22 07:25:22 2024 +0000
+++ b/macros.xml	Fri Nov 01 08:19:40 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 18e13043167d -r 1b4881c150cc mfassignr_findRecalSeries.xml
--- a/mfassignr_findRecalSeries.xml	Tue Oct 22 07:25:22 2024 +0000
+++ b/mfassignr_findRecalSeries.xml	Fri Nov 01 08:19:40 2024 +0000
@@ -12,53 +12,44 @@
     </edam_operations>
     <expand macro="creator" />
     <expand macro="refs" />
+    <expand macro="requirements" />
 
-    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         Rscript -e 'packageVersion("MFAssignR")' &&
         Rscript '${mfassignr_findrecalseries}'
     ]]>
     </command>
+
     <configfiles>
         <configfile name="mfassignr_findrecalseries"><![CDATA[
             library(dplyr)
             df <- read.table("$input_file", header=TRUE, sep="\t")
-            result <- MFAssignR::FindRecalSeries(
-                df = df,
-                global_min = $global_min,
-                global_max = $global_max,
-                number_of_combinations = $number_of_combinations,
-                abundance_score_threshold = $abundance_score_threshold,
-                peak_distance_threshold = $peak_distance_threshold,
-                coverage_threshold = $coverage_threshold,
-                fill_series = $fill_series
-            ) |> dplyr::rename(Series = series)
-            
+            result <- MFAssignR::FindRecalSeriesSimple(df) |> dplyr::slice(-1)
             write.table(result, file="$final_series", sep="\t", row.names=FALSE)
         ]]></configfile>
     </configfiles>
+
     <inputs>
-        <expand macro="findrecalseries_param"/>
+        <param name="input_file" type="data" format="tabular" label="Input data"
+        help="Recalibration series, output from RecalList"/>
     </inputs>
+
     <outputs>
         <data name="final_series" format="tabular" label="Final recalibration series"/>
     </outputs>
+
     <tests>
         <test>
             <param name="input_file" value="recallist/recal_series.tabular"/>
-            <param name="global_min" value="100"/>
-            <param name="global_max" value="500"/>
-            <param name="abundance_score_threshold" value="50"/>
-            <param name="number_of_combinations" value="3"/>
-            <param name="coverage_threshold" value="50"/>
-            <param name="fill_series" value="TRUE"/>
-            <output name="final_series" file="findrecalseries/selected_series.tabular"/>
+            <output name="final_series" file="findrecalseries/selected_series_simple.tabular"/>
         </test>
     </tests>
+
     <help>
         @FINDRECALSERIES_HELP@
 
         @GENERAL_HELP@
     </help>
+
     <expand macro="citations"/>
 </tool>
diff -r 18e13043167d -r 1b4881c150cc 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 08:19:40 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 18e13043167d -r 1b4881c150cc test-data/isofiltr/iso_out.tabular
--- a/test-data/isofiltr/iso_out.tabular	Tue Oct 22 07:25:22 2024 +0000
+++ b/test-data/isofiltr/iso_out.tabular	Fri Nov 01 08:19:40 2024 +0000
@@ -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"
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 233.156873358746	953506796.058272	221.997813102967	"C13"
-233.164518791019	2377175.5732822	351.160198568355	"2C13_S34"
+233.164518791019	2377175.5732822	351.160198568355	"C13_S34"
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 234.007662297674	3130283.5615464	387.961717539371	"C13"
@@ -1006,6 +1005,8 @@
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+266.137944674817	15583537.6586698	644.318859411887	"S34"
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 266.14610143058	31919885.9936052	605.965387703099	"C13"
 266.156008135692	4026363.12702958	771.121104816267	"C13"
@@ -1052,7 +1053,7 @@
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 270.095529546647	4738043.6436134	507.612394817294	"S34"
-270.11161023685	29003399.3628645	193.827926444867	"2C13"
+270.11161023685	29003399.3628645	193.827926444867	"2C13_S34"
 270.112209179863	30332528.0082494	572.962468086796	"2C13_S34"
 270.113400603345	8309656.23723502	573.5095992148	"S34"
 270.115780248034	26701911.1072602	189.319616541621	"C13"
@@ -1097,6 +1098,7 @@
 275.113079053009	45686645.1654632	221.521345551286	"C13"
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+275.163915496552	4208787.41202026	992.1609078	"S34"
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 275.1669710015	71625418.79991	210.229911334887	"C13"
 275.166974814798	44474240.1813179	616.158869844466	"C13"
@@ -1126,7 +1128,7 @@
 277.200682113452	3996097.8905666	568.273413548114	"S34"
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 278.120786510782	66847605.2781117	283.755980937194	"C13"
-278.12078765322	30196447.2482079	385.056241829711	"C13"
+278.12078765322	30196447.2482079	385.056241829711	"C13_S34"
 278.1214095	11248989.5807277	327.364083525523	"C13_S34"
 278.146309979218	131280664.687718	615.9269085	"C13"
 278.183040258862	11836995.1899958	639.247835352584	"C13"
@@ -1144,7 +1146,7 @@
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 280.104980547009	517650650.167541	1319.41470464764	"C13"
 280.136426533088	117552794.304774	244.217300981983	"C13"
-280.136432106673	25739539.4614655	878.591658222163	"C13"
+280.136432106673	25739539.4614655	878.591658222163	"C13_S34"
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@@ -1233,6 +1235,8 @@
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+289.142578263216	2174194.1680763	570.363678656577	"S34"
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 289.15445489322	7195495.85029992	600.197256801317	"2C13_S34"
@@ -1254,8 +1258,8 @@
 291.169401540441	2677443.08984007	206.998093005079	"S34"
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-291.170071737031	13596319.2544785	572.712665772014	"2C13"
-291.170073409332	11280383.1142331	724.40080556417	"2C13"
+291.170071737031	13596319.2544785	572.712665772014	"2C13_S34"
+291.170073409332	11280383.1142331	724.40080556417	"2C13_S34"
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 291.199407013227	69867655.5648707	307.75313059224	"C13"
 291.199409908068	339453654.559453	631.585634432429	"C13"
@@ -1273,6 +1277,7 @@
 292.174736545491	18206010.3146186	729.3605171	"S34"
 292.175404495074	8972775.64771223	499.754674195626	"S34"
 292.175405035184	12370393.7766547	530.187713967296	"S34"
+292.190151004457	168697654.660698	534.321359307745	"S34"
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@@ -1430,10 +1435,12 @@
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+308.293986395669	1981154.85339884	856.3934999	"S34"
 308.889032239181	8550877.95397492	1172.94424617242	"S34"
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+309.1223375	13243917.954223	176.595264179632	"S34"
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 309.15436343529	39505774.3778621	178.202061645368	"C13"
@@ -1487,6 +1494,7 @@
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 317.214899485481	58479830.9	375.533370540488	"C13"
@@ -1507,10 +1515,11 @@
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@@ -1524,6 +1533,7 @@
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@@ -1627,7 +1637,7 @@
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@@ -1643,7 +1653,7 @@
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@@ -1652,10 +1662,11 @@
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@@ -1707,8 +1718,10 @@
 350.203181467142	42627789.3248658	673.4855874	"C13"
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 479.266996055467	36369628.7434497	604.395338830877	"C13"
 479.266997002944	109334795.547706	648.879970835553	"C13"
 479.29937954355	12720574.0217518	561.013230241926	"C13"
+479.312050732579	3207024.51611706	406.486448037546	"S34"
 482.135117433278	3192604.28716499	508.986092922744	"C13"
 483.16955459511	4289567.64305926	292.566445695472	"C13"
 483.237975188856	28975700.2017335	632.257381918728	"S34"
@@ -2446,6 +2492,7 @@
 488.334114069463	19496999.3552835	882.4803052	"C13"
 489.336283434152	900649.6811	880.44077680398	"2C13"
 490.169653062943	3275269.22308749	618.890721540511	"S34"
+490.24101462448	2461536.37738184	151.518056081121	"S34"
 490.242470396731	27871109.2248715	394.493316923744	"S34"
 491.265137144474	55611197.9559347	559.466040819332	"C13"
 491.266598292691	34882891.1772035	562.944571	"C13"
diff -r 18e13043167d -r 1b4881c150cc test-data/isofiltr/mono_out.tabular
--- a/test-data/isofiltr/mono_out.tabular	Tue Oct 22 07:25:22 2024 +0000
+++ b/test-data/isofiltr/mono_out.tabular	Fri Nov 01 08:19:40 2024 +0000
@@ -1947,6 +1947,7 @@
 198.123260770412	13574394.4788487	261.059000792104
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 198.1236353835	127407296.13947	332.259128714369
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 198.148709916532	1563215.4176542	284.949069760009
 198.148711908004	149811824.857192	538.2576106
@@ -3808,8 +3809,6 @@
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 266.142022501628	45691747.5730606	555.380068655572
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@@ -4049,7 +4048,6 @@
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 309.133223042925	14166454.6571403	1318.19894239493
@@ -5306,7 +5299,6 @@
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@@ -5371,6 +5363,7 @@
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@@ -5437,7 +5428,6 @@
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@@ -6149,14 +6138,12 @@
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 438.217616735525	1855228.59370247	733.109037535555
 438.231154605326	164841475.089637	492.805761237962
 438.232388159591	153733929.933031	646.508964287327
@@ -8129,8 +8093,6 @@
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 440.299220569278	72863040.3902075	716.249745482826
 440.300458647041	22217067.3914832	643.453536071447
@@ -8312,7 +8274,6 @@
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 448.223845727225	613150474.952701	548.856347919696
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 448.253136	703622013.530404	596.2302015
 448.253136904259	552946903.4	676.265510154268
 448.262047255514	18838277.2063315	382.159805794382
@@ -8502,7 +8463,6 @@
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 458.272500365262	41761704.3912534	427.730421733596
 458.272508354303	15896516.4443566	985.914241607703
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 458.309366814416	97834203.36	704.91257448871
 458.319899888883	45454583.4316254	664.185511302196
@@ -8580,7 +8540,6 @@
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 462.306217342091	5605968.81457093	408.619380083753
 462.306218279134	4106842.16194794	490.288455761068
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 463.088858696242	4487114.62368511	454.75048830377
 463.128985480723	1702608.97878654	868.4503548
@@ -8638,10 +8597,8 @@
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 466.128538697439	481693.348890603	434.198240393334
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 466.227138051183	464338840.717891	475.749897987666
@@ -8856,13 +8813,10 @@
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 479.296566131505	21964307.9044292	731.85520874306
 479.3092372	31904404.07	631.273216553137
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 479.334587436396	10737427.1841608	742.966237195642
 480.149584476662	126887128.223587	216.957207158715
 480.186294338078	235747234.340003	437.016099676598
@@ -9037,7 +8991,6 @@
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 490.229369128826	44393551.243901	852.763324693888
 490.236640212202	371470428.295075	149.8837309
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 490.243927997779	3918842.56299929	460.908532847505
 490.246845913072	9644772.448	706.92319362724
 490.258496152149	9492623.14840407	564.222679250139
diff -r 18e13043167d -r 1b4881c150cc test-data/snplot/plot.png
Binary file test-data/snplot/plot.png has changed