diff riassigner_from_comment.xml @ 0:6975af39ba79 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit de7fd0986bce8d42bc7e63f9e4caf3c23862e497

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/riassigner_from_comment.xml	Thu Feb 22 10:40:33 2024 +0000
@@ -0,0 +1,73 @@
+<tool id="riassigner_from_comment" name="RIAssigner init from comment" version="@TOOL_VERSION@+galaxy4" profile="21.09">
+    <description>Assign different retention indices from unstructured comment metadata</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <xrefs>
+        <xref type="bio.tools">riassigner</xref>
+    </xrefs>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python ${script} &&
+        mv results.${input.ext} ${output}
+        ]]>
+    </command>
+
+    <configfiles>
+        <configfile name="script">
+from RIAssigner.data import PandasData, MatchMSData
+#if $input.ext in ["csv", "tsv", "parquet"]
+query = PandasData('${input}', '${input.ext}', rt_unit="seconds")
+#else
+query = MatchMSData('${input}', '${input.ext}', rt_unit="seconds")
+#end if
+query.init_ri_from_comment('${format}')
+query.write('results.${input.ext}')
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param name="input" type="data" format="csv,tsv,parquet,msp,mgf" label="Input File">
+            <help>
+                File with 'comment' metadata in which to assign the selected retention index type from 'comment' to 'retention_index'.
+            </help>
+        </param>
+        <param name="format" type="select" label="GC column type" help="Type of gas chromatographic column for which to set the retention index value">
+            <option value="SemiStdNP">Semi Standard Non-Polar</option>
+            <option value="StdNP">Standard Non-Polar</option>
+            <option value="StdPolar">Standard Polar</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format_source="input" name="output" label="${on_string} with ${format} RI"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="nist_to_ri_2mols_input.csv" ftype="csv"/>
+            <output name="output" file="nist_to_ri_2mols_output.csv" ftype="csv"/>
+        </test>
+        <test>
+            <param name="input" value="nist_ei_ms_2mols_input.msp" ftype="msp"/>
+            <output name="output" file="nist_ei_ms_2mols_output.msp" ftype="msp"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        This tool can be used to assign retention indices (RI) from the comment field in csv, tsv, parquet, or msp files.
+        The tool will read RI from the comment field and assign them to the RI field. The type of gas chromatographic column
+        for which to set the retention index value can be selected.
+    ]]></help>
+    
+    <citations>
+        <citation type="doi">10.21105/joss.04337</citation>
+    </citations>
+</tool>
+