Merge pull request #565 from zargham-ahmad/mfassignr-tools

Mfassignr ISOFiltr tool

tools/mfassignr/.shed.yml

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+name: MFAssignR
+owner: recetox
+remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr"
+homepage_url: "https://github.com/RECETOX/MFAssignR"
+categories:
+  - Metabolomics
+description: "The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements"
+long_description: |
+ "The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements. 
+ A number of tools for internal mass recalibration, MF assignment, signal-to-noise evaluation, and unambiguous MF assignments are provided. "
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }} tool from the MFAssignR package"
+suite:
+  name: suite_mfassignr
+  description: tools from MFAssignR are used for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements.
+  type: repository_suite_definition

tools/mfassignr/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">1.0.3</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="refs">
+        <xrefs>
+               <xref type="bio.tools">mfassignr</xref>
+        </xrefs>
+    </xml>
+
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Zargham"
+                familyName="Ahmad"
+                url="https://github.com/zargham-ahmad"
+                identifier="0000-0002-6096-224X" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="[email protected]"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
+    <xml name="isofiltr_param">
+        <param name="peaks" type="data" format="tabular" label="Input Peak Data"
+        help="The input data frame containing abundance and peak mass."/>
+        <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio"
+        help="Sets the noise cut for the data; peaks below this value will not be evaluated."/>
+        <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio"
+        help="Sets the maximum allowed ratio for matching 13C isotopes."/>
+        <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio"
+        help="Sets the maximum allowed ratio for matching 34S isotopes."/>
+        <param name="Sulferr" type="float" value="5" label="Maximum Error for 34S Matching (ppm)"
+        help="Sets the maximum allowed error (ppm) for 34S mass matching."/>
+        <param name="Carberr" type="float" value="5" label="Maximum Error for 13C Matching (ppm)"
+        help="Sets the maximum allowed error (ppm) for 13C mass matching."/>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1016/j.envres.2020.110114</citation>
+        </citations>        
+    </xml>
+
+</macros>

tools/mfassignr/mfassignr_isofiltr.xml

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+<tool id="mfassignr_isofiltr" name="MFAssignR IsoFiltR" version="@TOOL_VERSION@+galaxy0">
+    <description>
+        IsoFiltR separates likely isotopic masses from monoisotopic masses in a mass list.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator" />
+    <expand macro="refs" />
+
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript
+            -e 'source("${mfassignr_isofiltr}")'
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="mfassignr_isofiltr"><![CDATA[
+            peaks <- read.table("$peaks", header=TRUE, sep="\t")
+            result <- MFAssignR::IsoFiltR(
+                peaks = peaks,
+                SN = $SN,
+                Carbrat = $Carbrat,
+                Sulfrat = $Sulfrat,
+                Sulferr = $Sulferr,
+                Carberr = $Carberr
+            )
+            
+            write.table(result[["Mono"]], file="$mono_out", sep="\t", row.names=FALSE)
+            write.table(result[["Iso"]], file="$iso_out", sep="\t", row.names=FALSE)
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="isofiltr_param"/>
+    </inputs>
+    <outputs>
+        <data name="mono_out" format="tabular" label="Monoisotopic Masses"/>
+        <data name="iso_out" format="tabular" label="Isotopic Masses"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="peaks" value="QC1_1_POS_500.tabular" ftype="tabular"/>
+            <output name="mono_out" file="isofiltr_output1.tabular" ftype="tabular"/>
+            <output name="iso_out" file="isofiltr_output2.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+        IsoFiltR identifies and separates likely isotopic masses from monoisotopic masses in a mass list. 
+        This should be done prior to formula assignment to reduce incorrect formula assignments.
+
+        The input is a table containing abundance and peak mass in the following format:
+
+        +--------------------+-------------------+------------------------+
+        | mz                 | area              | rt                     |
+        +====================+===================+========================+
+        | 110.03486266079899 | 3410926.862054969 | 190.03735922916195     |
+        +--------------------+-------------------+------------------------+
+        | 110.05988136843429 | 7658687.858       | 241.17645551084158     |
+        +--------------------+-------------------+------------------------+
+        | ...                | ...               | ...                    |
+        +--------------------+-------------------+------------------------+
+    </help>
+    <expand macro="citations"/>
+</tool>