diff mfassignr_findRecalSeries.xml @ 4:1b4881c150cc draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030

--- 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>