diff mfassignr_recal.xml @ 0:235878c45443 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_recal.xml	Thu Aug 15 12:01:44 2024 +0000
@@ -0,0 +1,98 @@
+<tool id="mfassignr_recal" name="MFAssignR Recal" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+    <description>Internal mass recalibration using a recalibrant series.</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")
+            peaks <- read.delim("$peaks", sep="\t")
+            SN <- $sn_ratio * $kmdn
+
+            series <- read.delim('$series', sep='\t')
+
+            recal <- MFAssignR::Recal(
+                df = df,
+                peaks = peaks,
+                #if $isopeaks
+                isopeaks = read.delim("$isopeaks", sep="\t"),
+                #end if
+                mode = "$ionmode",
+                SN = SN,
+                mzRange = $mzRange,
+                step_O = $step_O,
+                step_H2 = $step_H2,
+                CalPeak = $CalPeak,
+                series1 = series[1, "Series"],
+                series2 = series[2, "Series"],
+                series3 = series[3, "Series"],
+                series4 = series[4, "Series"],
+                series5 = series[5, "Series"],
+                series6 = series[6, "Series"],
+                series7 = series[7, "Series"],
+                series8 = series[8, "Series"],
+                series9 = series[9, "Series"],
+                series10 = series[10, "Series"]
+            )
+
+            write.table(recal[['Mono']], file = '$Mono', row.names= FALSE, sep="\t")
+            write.table(recal[['Iso']], file = '$Iso', row.names= FALSE, sep="\t")
+            write.table(recal[['RecalList']], file = '$Recalibrants', row.names= FALSE, sep="\t")
+            ggplot2::ggsave(filename = "MZplot.png", recal[['Plot']])
+
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="recal_param"/>
+    </inputs>
+    <outputs>
+        <data name="Mono" format="tabular" label="Recalibrated 'Mono' list by ${tool.name} on ${on_string}"/>
+        <data name="Iso" format="tabular" label="Recalibrated 'Iso' list by ${tool.name} on ${on_string}"/>
+        <data name="Recalibrants" format="tabular" label="Recalibrants list (RecalOut) by ${tool.name} on ${on_string}"/>
+        <data name="MZplot" format="png" label="MZ plot by ${tool.name} on ${on_string}" from_work_dir="MZplot.png"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="mfassigncho/unambig.tabular"/>
+            <param name="series" value="recallist/recal_series.tabular"/>
+            <param name="peaks" value="isofiltr/mono_out.tabular"/>              
+            <param name="isopeaks" value="isofiltr/iso_out.tabular"/>
+            <output name="Mono">
+                <assert_contents>
+                    <has_n_lines n="9203"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output name="Iso">
+                <assert_contents>
+                    <has_n_lines n="2474"/>
+                    <has_n_columns n="4"/>
+                </assert_contents>
+            </output>
+            <output name="Recalibrants" file="recal/recalibrants.tabular"/>
+            <output name="MZplot">
+                <assert_contents>
+                    <has_size size="91080" delta="200"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        @RECAL_HELP@
+
+        @GENERAL_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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