--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfmid.xml	Wed Nov 15 16:28:04 2023 +0000
@@ -0,0 +1,115 @@
+<tool id="cfmid" name="CFM-ID" version="33">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="33">cfm</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        #set $tool_directory = $getVar('__tool_directory__', '../../../../tools/cfm')
+        python $tool_directory/cfmid.py
+            --input "$input"
+            --db_local '$db_local'
+            --ppm_db $ppm_db
+            --num_highest $num_highest
+            --ppm_mass_tol $ppm_mass_tol
+            --abs_mass_tol $abs_mass_tol
+            --polarity $polarity
+            --score_type $score_type
+            --results '$results'
+            --tool_directory '$tool_directory'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/>
+        <param argument="--db_local" type="data" format="tsv,tabular" label="Local Database (CSV)"/>
+        <param argument="--ppm_db" type="float" value="5.0" label="Mass tolerance in ppm to use when matching candidates in the database"/>
+        <param argument="--num_highest" type="integer" value="10" label="The number of (ranked) candidates to return"/>
+        <param argument="--ppm_mass_tol" type="float" value="10.0" label="Mass tolerance in ppm to use when matching peaks within the dot product comparison"/>
+        <param argument="--abs_mass_tol" type="float" value="0.01" label="Mass tolerance in abs Da to use when matching peaks within the dot product comparison (will use higher resulting tolerance of ppm and abs)"/>
+        <param argument="--polarity" type="select" label="Ion Mode">
+            <option value="pos" selected="true">Positive</option>
+            <option value="neg">Negative</option>
+        </param>
+        <param argument="--score_type" type="select" label="The type of scoring function to use when comparing spectra">
+            <option value="Jaccard" selected="true">Jaccard index</option>
+            <option value="DotProduct">Dot Product</option>
+        </param>
+        <param argument="--prob_thresh" type="float" value="0.001" label="The probability below which to prune unlikely fragmentations"/>
+    </inputs>
+    <outputs>
+        <data name="results" format="tsv" label="${tool.name} on ${on_string}: Annotations" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.msp"/>
+            <param name="db_local" value="db.tsv"/>
+            <param name="ppm_db" value="10.0"/>
+            <output name="results" file="annotations.tsv"/>
+        </test>
+    </tests>
+    <help>
+------
+CFM-ID
+------
+
+Description
+-----------
+
+Galaxy wrapper for CFM-ID tool. CFM-ID provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS). The program uses Competitive Fragmentation Modeling to produce a probabilistic generative model for the MS/MS fragmentation process and machine learning techniques to adapt the model parameters from data.
+
+Website: https://web.archive.org/web/20230827220748/https://cfmid.wishartlab.com/
+
+Parameters
+----------
+
+**\1. MSP file**
+
+MSP file
+
+**\2. Database containing InChI (or SMILES)**
+
+The database is used to fetch the candidates for the precursor. The candidates are "in silico" fragmented by CFMID and then the spectras are matched against those in the MSP.
+
+Custom database file in **tsv** or "tabular" format with the following structure:
+
++-------------+------------------+----------+---------------------------------------------+----------------------+
+| Identifier  | MonoisotopicMass | SMILES   | InChI                                       | Name                 |
++-------------+------------------+----------+---------------------------------------------+----------------------+
+| HMDB0000123 | 75.03202841      | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)  | Glycine              |
++-------------+------------------+----------+---------------------------------------------+----------------------+
+| HMDB0002151 | 78.0139355       | CS(C)=O  | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3             | Dimethyl sulfoxide   |
++-------------+------------------+----------+---------------------------------------------+----------------------+
+| ...         | ...              | ...      | ...                                         | ...                  |
++-------------+------------------+----------+---------------------------------------------+----------------------+
+
+**\3. Mass tolerance in ppm to use when matching candidates to the database**
+
+**\4. Mass tolerance in ppm to use when matching peaks within the Dot Product comparison**
+
+**\5. The number of (ranked) candidates to return**
+
+Set the top X candidates to return or use "-1" to return all of them, including those that the score is 0.
+
+**\6. Ion Mode**
+
+* Positive: For [M+H]+ adduct.
+
+* Negative: For [M-H]- adduct.
+
+**\7. The type of scoring function to use when comparing spectra**
+
+* Jaccard: The Jaccard coefficient measures similarity between finite sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets.
+
+* Dot Product: The product of the Euclidean magnitudes of the two vectors and the cosine of the angle between them.
+
+
+Developers and contributors
+---------------------------
+
+- **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
+- **Matthias Bernt** (m.bernt@ufz.de) - Helmholtz Centre for Environmental Research - UFZ
+- **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gku436</citation>
+    </citations>
+</tool>