Mercurial > repos > recetox > mfassignr_findrecalseries

changeset 4:1b4881c150cc draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030
author recetox
date Fri, 01 Nov 2024 08:19:40 +0000
parents 18e13043167d
children
files macros.xml mfassignr_findRecalSeries.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 6 files changed, 99 insertions(+), 117 deletions(-) [+]
line wrap: on
line diff
--- 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"/>
--- 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>
--- /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
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--- 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 @@
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@@ -737,7 +736,7 @@
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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"
--- 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 @@
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@@ -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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@@ -4555,7 +4551,6 @@
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@@ -5057,7 +5052,6 @@
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@@ -5069,7 +5063,6 @@
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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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@@ -5972,7 +5962,6 @@
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@@ -6149,14 +6138,12 @@
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 438.231154605326	164841475.089637	492.805761237962
 438.232388159591	153733929.933031	646.508964287327
@@ -8129,8 +8093,6 @@
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@@ -8312,7 +8274,6 @@
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 448.262047255514	18838277.2063315	382.159805794382
@@ -8502,7 +8463,6 @@
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 458.319899888883	45454583.4316254	664.185511302196
@@ -8580,7 +8540,6 @@
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@@ -8638,10 +8597,8 @@
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 466.227138051183	464338840.717891	475.749897987666
@@ -8856,13 +8813,10 @@
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 480.149584476662	126887128.223587	216.957207158715
 480.186294338078	235747234.340003	437.016099676598
@@ -9037,7 +8991,6 @@
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 490.246845913072	9644772.448	706.92319362724
 490.258496152149	9492623.14840407	564.222679250139
Binary file test-data/snplot/plot.png has changed