diff mfassignr_recallist.xml @ 0:6e1813883a9a draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mfassignr_recallist.xml	Thu Aug 15 12:00:39 2024 +0000
@@ -0,0 +1,47 @@
+<tool id="mfassignr_recallist" name="MFAssignR RecalList" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+    <description>Identification of candidate 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="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '${run_script}'
+    ]]></command>
+    <configfiles>
+        <configfile name="run_script"><![CDATA[
+            df <- read.delim("$input_file", sep="\t")
+            recal <- MFAssignR::RecalList(
+                df = df
+            )
+
+            write.table(recal, file = '$recal_series', row.names= FALSE, sep = "\t")
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="input_file" type="data" format="tabular" label="Input data"
+               help= "Input data frame - output from MFAssign or MFAssignCHO. Recommended are 'Unambiguous' assignments."/>
+    </inputs>
+    <outputs>
+        <data name="recal_series" format="tabular" label="Recalibration series by ${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="mfassigncho/unambig.tabular" />
+            <output name="recal_series" file="recallist/recal_series.tabular" lines_diff="100"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        @RECALLIST_HELP@
+
+        @GENERAL_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file