diff compound_identification.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compound_identification.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,105 @@
+<tool id="secimtools_compound_identification" name="Compound Identification" version="@WRAPPER_VERSION@">
+    <description>based on m/z ratio and retention time.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+compound_identification.py
+--anno $anno
+--uniqID $uniqID
+--mzID $mzID
+--rtID $rtID
+--library $library
+--libuniqID $libuniqID
+--libmzID $libmzID
+--librtID $librtID
+--output $output
+    ]]></command>
+    <inputs>
+        <param name="anno" type="data" format="tabular" label="Target Annotation File" help="Input tab-separated dataset in wide format. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" optional="false" label="Target Annotation Unique Feature ID column" help="Name of the column in your target annotation file containing unique identifiers."/>
+        <param name="mzID" type="text" size="30" value="" optional="false" label="Target Annotation Mass/Charge column." help="Name of the column in your target annotation file containing m/z ratios."/>
+        <param name="rtID" type="text" size="30" value="" optional="false" label="Target Annotation Retention Time" help="Name of the column in your target annotation file containing retention times."/>
+        <param name="library" type="data" format="tabular" label="Library File" help="Library dataset. If not tab separated see TIP below."/>
+        <param name="libuniqID" type="text" size="30" value="" optional="false" label="Library compound name column" help="Name of the column in your library file containing the compound/adduct names to use for identification."/>
+        <param name="libmzID" type="text" size="30" value="" optional="false" label="Library Mass/Charge column" help="Name of the column in your library file containing m/z ratios."/>
+        <param name="librtID" type="text" size="30" value="" optional="false" label="Library Retention Time column" help="Name of the column in your library file containing the retention times."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="identified_compounds_adducts_on_${anno.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="anno"      value="TEST0000_mzrt_first.tsv"/>
+            <param name="uniqID"    value="rowID_first"/>
+            <param name="mzID"      value="MZ_first" />
+            <param name="rtID"      value="RT_first" />
+            <param name="library"   value="TEST0000_database.tsv"/>
+            <param name="libuniqID" value="name_database"/>
+            <param name="libmzID"   value="MZ_database" />
+            <param name="librtID"   value="RT_database" />
+            <output name="output"   file="TEST0000_compound_identification_output.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+This tool is primarily intended for identification of compounds in a target file given a mass spectroscopy library file.
+
+Each metabolite (feature) is characterized by a mass to charge (m/z) ratio and retention time (RT).
+
+This tool matches two files: (1) a mass spectroscopy library file and (2) a target annotation file.
+
+The library file (in tsv format) contains a list of compounds and their associated m/z ratios and RTs.
+
+The target annotation file (in tsv format) contains the m/z ratios and RTs for the experimental samples.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required, a library file and an annotation target file.
+
+@MZRTFILE@
+
+**Target Annotation Unique Feature ID column**
+
+    - Name of the column in your target annotation file containing unique ID.
+
+
+**Annotation Mass/Charge column**
+
+    - Name of the column in your target annotation file containing the m/z ratio.
+
+**Annotation Retention Time**
+
+    - Name of the column in your target annotation file containing Retention Times.
+
+**Library File**
+
+**Library compound name colum**
+
+    - Name of the column in your library file containing the compound names to use.
+
+**Library Mass/Charge column**
+
+    - Name of the column in your library file containing the m/z ratios.
+
+**Library Retention Time column**
+
+    - Name of the column in your library file containing Retention Times.
+
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+A TSV file containing the original target annotation input file plus an additional column containing the name of any compounds that were matched using the m/z ratio and RT.
+
+]]></help>
+    <expand macro="citations"/>
+</tool>