diff mfassignr_mfassign.xml @ 0:5aa9380f397b 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_mfassign.xml	Thu Aug 15 12:00:54 2024 +0000
@@ -0,0 +1,110 @@
+<tool id="mfassignr_mfassign" name="MFAssignR MFAssign" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+    <description>Molecular formula assignment.</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>help.xml</import>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3172</edam_topic>    
+    </edam_topics>
+    <expand macro="creator" />
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '${run_script}'
+    ]]></command>
+    <configfiles>
+        <configfile name="run_script"><![CDATA[
+        mono <- read.delim("$input_mono", sep="\t")
+        #if $input_iso
+        iso <- read.delim("$input_iso", sep="\t")
+        #end if
+        SN = $sn_ratio * $kmdn
+
+        MF_assign <- MFAssignR::MFAssign(
+            peaks = mono,
+            #if $input_iso
+            isopeaks = iso,
+            #end if
+            ionMode = "$ionmode",
+            lowMW = $lowMW,
+            highMW = $highMW,
+            ppm_err = $ppm_err,
+            SN = SN
+        )
+
+        write.table(MF_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t")
+        write.table(MF_assign[['Ambig']], file = '$Ambig', row.names= FALSE, sep = "\t")
+        write.table(MF_assign[['None']], file = '$None', row.names= FALSE, sep = "\t")
+
+        dir.create("plots")
+        ggplot2::ggsave(filename = file.path("plots", "msassign.png"), MF_assign[['MSAssign']])
+        ggplot2::ggsave(filename = file.path("plots", "errorMZ.png"), MF_assign[['Error']])
+        ggplot2::ggsave(filename = file.path("plots", "MSgroups.png"), MF_assign[['MSgroups']])
+        ggplot2::ggsave(filename = file.path("plots", "VK.png"), MF_assign[['VK']])
+
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="input_mono" type="data" format="tabular" label="Data frame of monoisotopic masses"
+               help= "Data frame containing recalibrated monoisotopic masses, output from the Recal function"/>
+        <param name="input_iso" optional="true" type="data" format="tabular" label="Data frame of isotopic masses"
+               help= "Data frame containing recalibrated isotopic masses, output from the Recal function"/>
+        <expand macro="mfassign_param"/>
+    </inputs>
+    <outputs>
+        <data name="Unambig" format="tabular" label="Unambiguous assignments by ${tool.name} on ${on_string}"/>
+        <data name="Ambig" format="tabular" label="Ambiguous assignments by ${tool.name} on ${on_string}"/>
+        <data name="None" format="tabular" label="Unassigned masses by ${tool.name} on ${on_string}"/>
+        <collection format="png" type="list" name="plots" label="Plots generated by ${tool.name} on ${on_string}">
+            <discover_datasets pattern="__designation_and_ext__" ext="png" directory="plots" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_mono" value="isofiltr/mono_out.tabular"/>
+            <param name="input_iso" value="isofiltr/iso_out.tabular"/>
+            <param name="kmdn" value="3294705.63963789"/>
+            <output name="Unambig" file="mfassign/unambig.tabular"/>
+            <output name="Ambig">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_n_columns n="53"/>
+                </assert_contents>
+            </output>
+            <output name="None">
+                <assert_contents>
+                    <has_n_lines n="5015"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="4">
+                <element name="MSgroups">
+                    <assert_contents>
+                        <has_size size="114675" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="VK">
+                    <assert_contents>
+                        <has_size size="424518" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="errorMZ">
+                    <assert_contents>
+                        <has_size size="548366" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="msassign">
+                    <assert_contents>
+                        <has_size size="84901" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>    
+    </tests>
+    <help><![CDATA[
+        @MFASSIGN_HELP@
+
+        @GENERAL_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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