diff mfassignr_findRecalSeries.xml @ 0:a26b860d6ce7 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit c6e502d8af84750003e4ba001c61817acedd1896

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mfassignr_findRecalSeries.xml	Fri Sep 13 10:08:49 2024 +0000
@@ -0,0 +1,64 @@
+<tool id="mfassignr_findRecalSeries" name="MFAssignR FindRecalSeries" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+    <description>Selects most suitable series for recalibration</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>help.xml</import>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3172</edam_topic>    
+    </edam_topics>
+    <edam_operations>  
+        <edam_operation>operation_3627</edam_operation>  
+    </edam_operations>
+    <expand macro="creator" />
+    <expand macro="refs" />
+
+    <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 = $fill_series
+            ) |> dplyr::rename(Series = series)
+            
+            write.table(result, file="$final_series", sep="\t", row.names=FALSE)
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="findrecalseries_param"/>
+    </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"/>
+        </test>
+    </tests>
+    <help>
+        @FINDRECALSERIES_HELP@
+
+        @GENERAL_HELP@
+    </help>
+    <expand macro="citations"/>
+</tool>